[INFO] fetching crate nale 0.1.2...
[INFO] testing nale-0.1.2 against master#0d162b25edd5bf0dba9a22e83b614f1113e90474 for pr-150681
[INFO] extracting crate nale 0.1.2 into /workspace/builds/worker-2-tc1/source
[INFO] started tweaking crates.io crate nale 0.1.2
[INFO] finished tweaking crates.io crate nale 0.1.2
[INFO] tweaked toml for crates.io crate nale 0.1.2 written to /workspace/builds/worker-2-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate nale 0.1.2 on toolchain 0d162b25edd5bf0dba9a22e83b614f1113e90474
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[INFO] [stdout] warning: use of deprecated trait `util::PrintMe`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/structs/bound.rs:1:18
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::util::PrintMe;
[INFO] [stdout]   |                  ^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `util::PrintMe`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/structs/bound.rs:40:6
[INFO] [stdout]    |
[INFO] [stdout] 40 | impl PrintMe for CloudBound {
[INFO] [stdout]    |      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/structs/dp_matrix_sparse.rs:2:32
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::structs::dp_matrix::DpMatrix;
[INFO] [stdout]   |                                ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/structs/dp_matrix_sparse.rs:3:21
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::structs::Profile;
[INFO] [stdout]   |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/structs/dp_matrix_sparse.rs:163:6
[INFO] [stdout]     |
[INFO] [stdout] 163 | impl DpMatrix for DpMatrixSparse {
[INFO] [stdout]     |      ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/structs/dp_matrix_sparse.rs:224:6
[INFO] [stdout]     |
[INFO] [stdout] 224 | impl DpMatrix for RefMut<'_, DpMatrixSparse> {
[INFO] [stdout]     |      ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/structs/dp_matrix_sparse.rs:211:37
[INFO] [stdout]     |
[INFO] [stdout] 211 |         debug_assert!(special_idx < Profile::NUM_SPECIAL_STATES);
[INFO] [stdout]     |                                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/structs/dp_matrix_sparse.rs:218:37
[INFO] [stdout]     |
[INFO] [stdout] 218 |         debug_assert!(special_idx < Profile::NUM_SPECIAL_STATES);
[INFO] [stdout]     |                                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/structs/dp_matrix_sparse.rs:272:37
[INFO] [stdout]     |
[INFO] [stdout] 272 |         debug_assert!(special_idx < Profile::NUM_SPECIAL_STATES);
[INFO] [stdout]     |                                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/structs/dp_matrix_sparse.rs:279:37
[INFO] [stdout]     |
[INFO] [stdout] 279 |         debug_assert!(special_idx < Profile::NUM_SPECIAL_STATES);
[INFO] [stdout]     |                                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated macro `util::max_f32`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/cloud_search_common.rs:2:12
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::max_f32;
[INFO] [stdout]   |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated macro `util::log_sum`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/forward_bounded.rs:2:12
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::log_sum;
[INFO] [stdout]   |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/forward_bounded.rs:3:32
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::structs::dp_matrix::DpMatrix;
[INFO] [stdout]   |                                ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/forward_bounded.rs:4:22
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/forward_bounded.rs:4:31
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/forward_bounded.rs:5:18
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::util::log_add;
[INFO] [stdout]   |                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/forward_bounded.rs:8:15
[INFO] [stdout]   |
[INFO] [stdout] 8 |     profile: &Profile,
[INFO] [stdout]   |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/forward_bounded.rs:9:14
[INFO] [stdout]   |
[INFO] [stdout] 9 |     target: &Sequence,
[INFO] [stdout]   |              ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:10:26
[INFO] [stdout]    |
[INFO] [stdout] 10 |     dp_matrix: &mut impl DpMatrix,
[INFO] [stdout]    |                          ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:15:52
[INFO] [stdout]    |
[INFO] [stdout] 15 |     dp_matrix.set_special(bounds.target_start - 1, Profile::SPECIAL_N_IDX, 0.0);
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:18:9
[INFO] [stdout]    |
[INFO] [stdout] 18 |         Profile::SPECIAL_B_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:19:42
[INFO] [stdout]    |
[INFO] [stdout] 19 |         profile.special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:19:66
[INFO] [stdout]    |
[INFO] [stdout] 19 |         profile.special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:23:9
[INFO] [stdout]    |
[INFO] [stdout] 23 |         Profile::SPECIAL_E_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:28:9
[INFO] [stdout]    |
[INFO] [stdout] 28 |         Profile::SPECIAL_C_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:33:9
[INFO] [stdout]    |
[INFO] [stdout] 33 |         Profile::SPECIAL_J_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:45:17
[INFO] [stdout]     |
[INFO] [stdout]  45 | /                 log_sum!(
[INFO] [stdout]  46 | |                     dp_matrix.get_match(target_idx - 1, profile_idx - 1)
[INFO] [stdout]  47 | |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]  48 | |                     dp_matrix.get_insert(target_idx - 1, profile_idx - 1)
[INFO] [stdout] ...   |
[INFO] [stdout]  53 | |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]  54 | |                 ) + profile.match_score(current_target_character as usize, profile_idx),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:47:52
[INFO] [stdout]    |
[INFO] [stdout] 47 |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:45:17
[INFO] [stdout]     |
[INFO] [stdout]  45 | /                 log_sum!(
[INFO] [stdout]  46 | |                     dp_matrix.get_match(target_idx - 1, profile_idx - 1)
[INFO] [stdout]  47 | |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]  48 | |                     dp_matrix.get_insert(target_idx - 1, profile_idx - 1)
[INFO] [stdout] ...   |
[INFO] [stdout]  53 | |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]  54 | |                 ) + profile.match_score(current_target_character as usize, profile_idx),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:49:52
[INFO] [stdout]    |
[INFO] [stdout] 49 |                         + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:45:17
[INFO] [stdout]     |
[INFO] [stdout]  45 | /                 log_sum!(
[INFO] [stdout]  46 | |                     dp_matrix.get_match(target_idx - 1, profile_idx - 1)
[INFO] [stdout]  47 | |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]  48 | |                     dp_matrix.get_insert(target_idx - 1, profile_idx - 1)
[INFO] [stdout] ...   |
[INFO] [stdout]  53 | |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]  54 | |                 ) + profile.match_score(current_target_character as usize, profile_idx),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:50:59
[INFO] [stdout]    |
[INFO] [stdout] 50 |                     dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]    |                                                           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:51:52
[INFO] [stdout]    |
[INFO] [stdout] 51 |                         + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:53:52
[INFO] [stdout]    |
[INFO] [stdout] 53 |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:61:17
[INFO] [stdout]     |
[INFO] [stdout]  61 | /                 log_sum!(
[INFO] [stdout]  62 | |                     dp_matrix.get_match(target_idx - 1, profile_idx)
[INFO] [stdout]  63 | |                         + profile.transition_score(Profile::MATCH_TO_INSERT_IDX, profile_idx),
[INFO] [stdout]  64 | |                     dp_matrix.get_insert(target_idx - 1, profile_idx)
[INFO] [stdout]  65 | |                         + profile.transition_score(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]  66 | |                 ) + profile.insert_score(current_target_character as usize, profile_idx),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:63:52
[INFO] [stdout]    |
[INFO] [stdout] 63 |                         + profile.transition_score(Profile::MATCH_TO_INSERT_IDX, profile_idx),
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:65:52
[INFO] [stdout]    |
[INFO] [stdout] 65 |                         + profile.transition_score(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:73:17
[INFO] [stdout]     |
[INFO] [stdout]  73 | /                 log_sum!(
[INFO] [stdout]  74 | |                     dp_matrix.get_match(target_idx, profile_idx - 1)
[INFO] [stdout]  75 | |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx - 1),
[INFO] [stdout]  76 | |                     dp_matrix.get_delete(target_idx, profile_idx - 1)
[INFO] [stdout]  77 | |                         + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]  78 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:75:52
[INFO] [stdout]    |
[INFO] [stdout] 75 |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx - 1),
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:77:52
[INFO] [stdout]    |
[INFO] [stdout] 77 |                         + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:84:17
[INFO] [stdout]    |
[INFO] [stdout] 84 |                 Profile::SPECIAL_E_IDX,
[INFO] [stdout]    |                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:85:17
[INFO] [stdout]     |
[INFO] [stdout]  85 | /                 log_sum!(
[INFO] [stdout]  86 | |                     dp_matrix.get_match(target_idx, profile_idx) + end_score,
[INFO] [stdout]  87 | |                     dp_matrix.get_delete(target_idx, profile_idx) + end_score,
[INFO] [stdout]  88 | |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]  89 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:85:17
[INFO] [stdout]     |
[INFO] [stdout]  85 | /                 log_sum!(
[INFO] [stdout]  86 | |                     dp_matrix.get_match(target_idx, profile_idx) + end_score,
[INFO] [stdout]  87 | |                     dp_matrix.get_delete(target_idx, profile_idx) + end_score,
[INFO] [stdout]  88 | |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]  89 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:88:55
[INFO] [stdout]    |
[INFO] [stdout] 88 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]    |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:99:13
[INFO] [stdout]     |
[INFO] [stdout]  99 | /             log_sum!(
[INFO] [stdout] 100 | |                 dp_matrix.get_match(target_idx - 1, last_profile_idx - 1)
[INFO] [stdout] 101 | |                     + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, last_profile_idx - 1),
[INFO] [stdout] 102 | |                 dp_matrix.get_insert(target_idx - 1, last_profile_idx - 1)
[INFO] [stdout] ...   |
[INFO] [stdout] 107 | |                     + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, last_profile_idx - 1)
[INFO] [stdout] 108 | |             ) + profile.match_score(current_target_character as usize, last_profile_idx),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:101:48
[INFO] [stdout]     |
[INFO] [stdout] 101 |                     + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, last_profile_idx - 1),
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:99:13
[INFO] [stdout]     |
[INFO] [stdout]  99 | /             log_sum!(
[INFO] [stdout] 100 | |                 dp_matrix.get_match(target_idx - 1, last_profile_idx - 1)
[INFO] [stdout] 101 | |                     + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, last_profile_idx - 1),
[INFO] [stdout] 102 | |                 dp_matrix.get_insert(target_idx - 1, last_profile_idx - 1)
[INFO] [stdout] ...   |
[INFO] [stdout] 107 | |                     + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, last_profile_idx - 1)
[INFO] [stdout] 108 | |             ) + profile.match_score(current_target_character as usize, last_profile_idx),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:103:48
[INFO] [stdout]     |
[INFO] [stdout] 103 |                     + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, last_profile_idx - 1),
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:99:13
[INFO] [stdout]     |
[INFO] [stdout]  99 | /             log_sum!(
[INFO] [stdout] 100 | |                 dp_matrix.get_match(target_idx - 1, last_profile_idx - 1)
[INFO] [stdout] 101 | |                     + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, last_profile_idx - 1),
[INFO] [stdout] 102 | |                 dp_matrix.get_insert(target_idx - 1, last_profile_idx - 1)
[INFO] [stdout] ...   |
[INFO] [stdout] 107 | |                     + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, last_profile_idx - 1)
[INFO] [stdout] 108 | |             ) + profile.match_score(current_target_character as usize, last_profile_idx),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:104:55
[INFO] [stdout]     |
[INFO] [stdout] 104 |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:105:48
[INFO] [stdout]     |
[INFO] [stdout] 105 |                     + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, last_profile_idx - 1),
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:107:48
[INFO] [stdout]     |
[INFO] [stdout] 107 |                     + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, last_profile_idx - 1)
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:118:13
[INFO] [stdout]     |
[INFO] [stdout] 118 | /             log_sum!(
[INFO] [stdout] 119 | |                 dp_matrix.get_match(target_idx, last_profile_idx - 1)
[INFO] [stdout] 120 | |                     + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, last_profile_idx - 1),
[INFO] [stdout] 121 | |                 dp_matrix.get_delete(target_idx, last_profile_idx - 1)
[INFO] [stdout] 122 | |                     + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, last_profile_idx - 1)
[INFO] [stdout] 123 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:120:48
[INFO] [stdout]     |
[INFO] [stdout] 120 |                     + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, last_profile_idx - 1),
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:122:48
[INFO] [stdout]     |
[INFO] [stdout] 122 |                     + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, last_profile_idx - 1)
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:129:13
[INFO] [stdout]     |
[INFO] [stdout] 129 |             Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:130:13
[INFO] [stdout]     |
[INFO] [stdout] 130 | /             log_sum!(
[INFO] [stdout] 131 | |                 dp_matrix.get_match(target_idx, last_profile_idx),
[INFO] [stdout] 132 | |                 dp_matrix.get_delete(target_idx, last_profile_idx),
[INFO] [stdout] 133 | |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout] 134 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:130:13
[INFO] [stdout]     |
[INFO] [stdout] 130 | /             log_sum!(
[INFO] [stdout] 131 | |                 dp_matrix.get_match(target_idx, last_profile_idx),
[INFO] [stdout] 132 | |                 dp_matrix.get_delete(target_idx, last_profile_idx),
[INFO] [stdout] 133 | |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout] 134 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:133:51
[INFO] [stdout]     |
[INFO] [stdout] 133 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:140:13
[INFO] [stdout]     |
[INFO] [stdout] 140 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:141:13
[INFO] [stdout]     |
[INFO] [stdout] 141 | /             log_sum!(
[INFO] [stdout] 142 | |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout] 143 | |                     + profile.special_transition_score(
[INFO] [stdout] 144 | |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout] ...   |
[INFO] [stdout] 152 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:142:55
[INFO] [stdout]     |
[INFO] [stdout] 142 |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:144:25
[INFO] [stdout]     |
[INFO] [stdout] 144 |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:145:25
[INFO] [stdout]     |
[INFO] [stdout] 145 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:147:51
[INFO] [stdout]     |
[INFO] [stdout] 147 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:149:25
[INFO] [stdout]     |
[INFO] [stdout] 149 |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:150:25
[INFO] [stdout]     |
[INFO] [stdout] 150 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:158:13
[INFO] [stdout]     |
[INFO] [stdout] 158 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:159:13
[INFO] [stdout]     |
[INFO] [stdout] 159 | /             log_sum!(
[INFO] [stdout] 160 | |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout] 161 | |                     + profile.special_transition_score(
[INFO] [stdout] 162 | |                         Profile::SPECIAL_C_IDX,
[INFO] [stdout] ...   |
[INFO] [stdout] 170 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:160:55
[INFO] [stdout]     |
[INFO] [stdout] 160 |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:162:25
[INFO] [stdout]     |
[INFO] [stdout] 162 |                         Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:163:25
[INFO] [stdout]     |
[INFO] [stdout] 163 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:165:51
[INFO] [stdout]     |
[INFO] [stdout] 165 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:167:25
[INFO] [stdout]     |
[INFO] [stdout] 167 |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:168:25
[INFO] [stdout]     |
[INFO] [stdout] 168 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:176:13
[INFO] [stdout]     |
[INFO] [stdout] 176 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:177:51
[INFO] [stdout]     |
[INFO] [stdout] 177 |             dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:179:47
[INFO] [stdout]     |
[INFO] [stdout] 179 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:179:71
[INFO] [stdout]     |
[INFO] [stdout] 179 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:185:13
[INFO] [stdout]     |
[INFO] [stdout] 185 |             Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/forward_bounded.rs:186:13
[INFO] [stdout]     |
[INFO] [stdout] 186 | /             log_sum!(
[INFO] [stdout] 187 | |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX)
[INFO] [stdout] 188 | |                     + profile.special_transition_score(
[INFO] [stdout] 189 | |                         Profile::SPECIAL_N_IDX,
[INFO] [stdout] ...   |
[INFO] [stdout] 197 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:187:51
[INFO] [stdout]     |
[INFO] [stdout] 187 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:189:25
[INFO] [stdout]     |
[INFO] [stdout] 189 |                         Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:190:25
[INFO] [stdout]     |
[INFO] [stdout] 190 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:192:51
[INFO] [stdout]     |
[INFO] [stdout] 192 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:194:25
[INFO] [stdout]     |
[INFO] [stdout] 194 |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:195:25
[INFO] [stdout]     |
[INFO] [stdout] 195 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:201:46
[INFO] [stdout]     |
[INFO] [stdout] 201 |     dp_matrix.get_special(bounds.target_end, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated macro `util::log_sum`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/backward_bounded.rs:2:12
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::log_sum;
[INFO] [stdout]   |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/backward_bounded.rs:3:32
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::structs::dp_matrix::DpMatrix;
[INFO] [stdout]   |                                ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/backward_bounded.rs:4:22
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/backward_bounded.rs:4:31
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/backward_bounded.rs:5:18
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::util::log_add;
[INFO] [stdout]   |                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/backward_bounded.rs:8:15
[INFO] [stdout]   |
[INFO] [stdout] 8 |     profile: &Profile,
[INFO] [stdout]   |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/backward_bounded.rs:9:14
[INFO] [stdout]   |
[INFO] [stdout] 9 |     target: &Sequence,
[INFO] [stdout]   |              ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:10:26
[INFO] [stdout]    |
[INFO] [stdout] 10 |     dp_matrix: &mut impl DpMatrix,
[INFO] [stdout]    |                          ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:41:9
[INFO] [stdout]    |
[INFO] [stdout] 41 |         Profile::SPECIAL_J_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:46:9
[INFO] [stdout]    |
[INFO] [stdout] 46 |         Profile::SPECIAL_B_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:51:9
[INFO] [stdout]    |
[INFO] [stdout] 51 |         Profile::SPECIAL_N_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:57:9
[INFO] [stdout]    |
[INFO] [stdout] 57 |         Profile::SPECIAL_C_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:58:42
[INFO] [stdout]    |
[INFO] [stdout] 58 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:58:66
[INFO] [stdout]    |
[INFO] [stdout] 58 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:63:9
[INFO] [stdout]    |
[INFO] [stdout] 63 |         Profile::SPECIAL_E_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:64:42
[INFO] [stdout]    |
[INFO] [stdout] 64 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]    |                                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:64:66
[INFO] [stdout]    |
[INFO] [stdout] 64 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]    |                                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:65:48
[INFO] [stdout]    |
[INFO] [stdout] 65 |             + profile.special_transition_score(Profile::SPECIAL_E_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:65:72
[INFO] [stdout]    |
[INFO] [stdout] 65 |             + profile.special_transition_score(Profile::SPECIAL_E_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:85:54
[INFO] [stdout]    |
[INFO] [stdout] 85 |         dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX),
[INFO] [stdout]    |                                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:91:54
[INFO] [stdout]    |
[INFO] [stdout] 91 |         dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX),
[INFO] [stdout]    |                                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:116:13
[INFO] [stdout]     |
[INFO] [stdout] 116 | /             log_sum!(
[INFO] [stdout] 117 | |                 dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout] 118 | |                 dp_matrix.get_delete(row_bounds.target_end, profile_idx + 1)
[INFO] [stdout] 119 | |                     + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout] 120 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:117:62
[INFO] [stdout]     |
[INFO] [stdout] 117 |                 dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]     |                                                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:119:48
[INFO] [stdout]     |
[INFO] [stdout] 119 |                     + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:127:13
[INFO] [stdout]     |
[INFO] [stdout] 127 | /             log_sum!(
[INFO] [stdout] 128 | |                 dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout] 129 | |                 dp_matrix.get_delete(row_bounds.target_end, profile_idx + 1)
[INFO] [stdout] 130 | |                     + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx)
[INFO] [stdout] 131 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:128:62
[INFO] [stdout]     |
[INFO] [stdout] 128 |                 dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]     |                                                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:130:48
[INFO] [stdout]     |
[INFO] [stdout] 130 |                     + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:161:13
[INFO] [stdout]     |
[INFO] [stdout] 161 |             Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:164:21
[INFO] [stdout]     |
[INFO] [stdout] 164 |                     Profile::BEGIN_TO_MATCH_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:175:17
[INFO] [stdout]     |
[INFO] [stdout] 175 |                 Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:176:17
[INFO] [stdout]     |
[INFO] [stdout] 176 | /                 log_sum!(
[INFO] [stdout] 177 | |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX),
[INFO] [stdout] 178 | |                     dp_matrix.get_match(target_idx + 1, profile_idx)
[INFO] [stdout] 179 | |                         + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout] 180 | |                         + profile.match_score(current_residue, profile_idx)
[INFO] [stdout] 181 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:177:55
[INFO] [stdout]     |
[INFO] [stdout] 177 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX),
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:179:52
[INFO] [stdout]     |
[INFO] [stdout] 179 |                         + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:187:13
[INFO] [stdout]     |
[INFO] [stdout] 187 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:188:13
[INFO] [stdout]     |
[INFO] [stdout] 188 | /             log_sum!(
[INFO] [stdout] 189 | |                 dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout] 190 | |                     + profile.special_transition_score(
[INFO] [stdout] 191 | |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout] ...   |
[INFO] [stdout] 199 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:189:55
[INFO] [stdout]     |
[INFO] [stdout] 189 |                 dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:191:25
[INFO] [stdout]     |
[INFO] [stdout] 191 |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:192:25
[INFO] [stdout]     |
[INFO] [stdout] 192 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:194:51
[INFO] [stdout]     |
[INFO] [stdout] 194 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:196:25
[INFO] [stdout]     |
[INFO] [stdout] 196 |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:197:25
[INFO] [stdout]     |
[INFO] [stdout] 197 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:204:13
[INFO] [stdout]     |
[INFO] [stdout] 204 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:205:51
[INFO] [stdout]     |
[INFO] [stdout] 205 |             dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:207:47
[INFO] [stdout]     |
[INFO] [stdout] 207 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:207:71
[INFO] [stdout]     |
[INFO] [stdout] 207 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:212:13
[INFO] [stdout]     |
[INFO] [stdout] 212 |             Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:213:13
[INFO] [stdout]     |
[INFO] [stdout] 213 | /             log_sum!(
[INFO] [stdout] 214 | |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout] 215 | |                     + profile.special_transition_score(
[INFO] [stdout] 216 | |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout] ...   |
[INFO] [stdout] 224 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:214:51
[INFO] [stdout]     |
[INFO] [stdout] 214 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:216:25
[INFO] [stdout]     |
[INFO] [stdout] 216 |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:217:25
[INFO] [stdout]     |
[INFO] [stdout] 217 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:219:51
[INFO] [stdout]     |
[INFO] [stdout] 219 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:221:25
[INFO] [stdout]     |
[INFO] [stdout] 221 |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:222:25
[INFO] [stdout]     |
[INFO] [stdout] 222 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:229:13
[INFO] [stdout]     |
[INFO] [stdout] 229 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:230:13
[INFO] [stdout]     |
[INFO] [stdout] 230 | /             log_sum!(
[INFO] [stdout] 231 | |                 dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout] 232 | |                     + profile.special_transition_score(
[INFO] [stdout] 233 | |                         Profile::SPECIAL_N_IDX,
[INFO] [stdout] ...   |
[INFO] [stdout] 241 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:231:55
[INFO] [stdout]     |
[INFO] [stdout] 231 |                 dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:233:25
[INFO] [stdout]     |
[INFO] [stdout] 233 |                         Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:234:25
[INFO] [stdout]     |
[INFO] [stdout] 234 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:236:51
[INFO] [stdout]     |
[INFO] [stdout] 236 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:238:25
[INFO] [stdout]     |
[INFO] [stdout] 238 |                         Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:239:25
[INFO] [stdout]     |
[INFO] [stdout] 239 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:247:47
[INFO] [stdout]     |
[INFO] [stdout] 247 |             dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:255:47
[INFO] [stdout]     |
[INFO] [stdout] 255 |             dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:262:17
[INFO] [stdout]     |
[INFO] [stdout] 262 | /                 log_sum!(
[INFO] [stdout] 263 | |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout] 264 | |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx)
[INFO] [stdout] 265 | |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout] 271 | |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout] 272 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:264:52
[INFO] [stdout]     |
[INFO] [stdout] 264 |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:262:17
[INFO] [stdout]     |
[INFO] [stdout] 262 | /                 log_sum!(
[INFO] [stdout] 263 | |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout] 264 | |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx)
[INFO] [stdout] 265 | |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout] 271 | |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout] 272 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:267:52
[INFO] [stdout]     |
[INFO] [stdout] 267 |                         + profile.transition_score(Profile::MATCH_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:262:17
[INFO] [stdout]     |
[INFO] [stdout] 262 | /                 log_sum!(
[INFO] [stdout] 263 | |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout] 264 | |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx)
[INFO] [stdout] 265 | |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout] 271 | |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout] 272 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:269:55
[INFO] [stdout]     |
[INFO] [stdout] 269 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:271:52
[INFO] [stdout]     |
[INFO] [stdout] 271 |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:278:17
[INFO] [stdout]     |
[INFO] [stdout] 278 | /                 log_sum!(
[INFO] [stdout] 279 | |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout] 280 | |                         + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, profile_idx)
[INFO] [stdout] 281 | |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout] 284 | |                         + profile.insert_score(current_residue, profile_idx)
[INFO] [stdout] 285 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:280:52
[INFO] [stdout]     |
[INFO] [stdout] 280 |                         + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:283:52
[INFO] [stdout]     |
[INFO] [stdout] 283 |                         + profile.transition_score(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:291:17
[INFO] [stdout]     |
[INFO] [stdout] 291 | /                 log_sum!(
[INFO] [stdout] 292 | |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout] 293 | |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx)
[INFO] [stdout] 294 | |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout] 297 | |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX) + end_score
[INFO] [stdout] 298 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:293:52
[INFO] [stdout]     |
[INFO] [stdout] 293 |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:291:17
[INFO] [stdout]     |
[INFO] [stdout] 291 | /                 log_sum!(
[INFO] [stdout] 292 | |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout] 293 | |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx)
[INFO] [stdout] 294 | |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout] 297 | |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX) + end_score
[INFO] [stdout] 298 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:296:52
[INFO] [stdout]     |
[INFO] [stdout] 296 |                         + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx),
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:297:55
[INFO] [stdout]     |
[INFO] [stdout] 297 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX) + end_score
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:310:9
[INFO] [stdout]     |
[INFO] [stdout] 310 |         Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:312:40
[INFO] [stdout]     |
[INFO] [stdout] 312 |             + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, 0)
[INFO] [stdout]     |                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:319:13
[INFO] [stdout]     |
[INFO] [stdout] 319 |             Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:320:13
[INFO] [stdout]     |
[INFO] [stdout] 320 | /             log_sum!(
[INFO] [stdout] 321 | |                 dp_matrix.get_special(row_bounds.target_start - 1, Profile::SPECIAL_B_IDX),
[INFO] [stdout] 322 | |                 dp_matrix.get_match(row_bounds.target_start, profile_idx)
[INFO] [stdout] 323 | |                     + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout] 324 | |                     + profile.match_score(first_target_character, profile_idx)
[INFO] [stdout] 325 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:321:68
[INFO] [stdout]     |
[INFO] [stdout] 321 |                 dp_matrix.get_special(row_bounds.target_start - 1, Profile::SPECIAL_B_IDX),
[INFO] [stdout]     |                                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:323:48
[INFO] [stdout]     |
[INFO] [stdout] 323 |                     + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:331:9
[INFO] [stdout]     |
[INFO] [stdout] 331 |         Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:336:9
[INFO] [stdout]     |
[INFO] [stdout] 336 |         Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:341:9
[INFO] [stdout]     |
[INFO] [stdout] 341 |         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:346:9
[INFO] [stdout]     |
[INFO] [stdout] 346 |         Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/backward_bounded.rs:347:9
[INFO] [stdout]     |
[INFO] [stdout] 347 | /         log_sum!(
[INFO] [stdout] 348 | |             dp_matrix.get_special(row_bounds.target_start, Profile::SPECIAL_N_IDX)
[INFO] [stdout] 349 | |                 + profile
[INFO] [stdout] 350 | |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout] ...   |
[INFO] [stdout] 353 | |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout] 354 | |         ),
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:348:60
[INFO] [stdout]     |
[INFO] [stdout] 348 |             dp_matrix.get_special(row_bounds.target_start, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:350:47
[INFO] [stdout]     |
[INFO] [stdout] 350 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:350:71
[INFO] [stdout]     |
[INFO] [stdout] 350 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:351:64
[INFO] [stdout]     |
[INFO] [stdout] 351 |             dp_matrix.get_special(row_bounds.target_start - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:353:47
[INFO] [stdout]     |
[INFO] [stdout] 353 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:353:71
[INFO] [stdout]     |
[INFO] [stdout] 353 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]     |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/posterior_bounded.rs:2:32
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::structs::dp_matrix::DpMatrix;
[INFO] [stdout]   |                                ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/posterior_bounded.rs:3:21
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::structs::Profile;
[INFO] [stdout]   |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/posterior_bounded.rs:6:15
[INFO] [stdout]   |
[INFO] [stdout] 6 |     profile: &Profile,
[INFO] [stdout]   |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/posterior_bounded.rs:7:27
[INFO] [stdout]   |
[INFO] [stdout] 7 |     forward_matrix: &impl DpMatrix,
[INFO] [stdout]   |                           ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/posterior_bounded.rs:8:28
[INFO] [stdout]   |
[INFO] [stdout] 8 |     backward_matrix: &impl DpMatrix,
[INFO] [stdout]   |                            ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/posterior_bounded.rs:9:33
[INFO] [stdout]   |
[INFO] [stdout] 9 |     posterior_matrix: &mut impl DpMatrix,
[INFO] [stdout]   |                                 ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:13:45
[INFO] [stdout]    |
[INFO] [stdout] 13 |         .get_special(row_bounds.target_end, Profile::SPECIAL_C_IDX)
[INFO] [stdout]    |                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:14:44
[INFO] [stdout]    |
[INFO] [stdout] 14 |         + profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX);
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:14:68
[INFO] [stdout]    |
[INFO] [stdout] 14 |         + profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX);
[INFO] [stdout]    |                                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:18:63
[INFO] [stdout]    |
[INFO] [stdout] 18 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_E_IDX, 0.0);
[INFO] [stdout]    |                                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:19:63
[INFO] [stdout]    |
[INFO] [stdout] 19 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_N_IDX, 0.0);
[INFO] [stdout]    |                                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:20:63
[INFO] [stdout]    |
[INFO] [stdout] 20 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_J_IDX, 0.0);
[INFO] [stdout]    |                                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:21:63
[INFO] [stdout]    |
[INFO] [stdout] 21 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_B_IDX, 0.0);
[INFO] [stdout]    |                                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:22:63
[INFO] [stdout]    |
[INFO] [stdout] 22 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_C_IDX, 0.0);
[INFO] [stdout]    |                                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:82:50
[INFO] [stdout]    |
[INFO] [stdout] 82 |         posterior_matrix.set_special(target_idx, Profile::SPECIAL_E_IDX, 0.0);
[INFO] [stdout]    |                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:86:13
[INFO] [stdout]    |
[INFO] [stdout] 86 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]    |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:87:57
[INFO] [stdout]    |
[INFO] [stdout] 87 |             (forward_matrix.get_special(target_idx - 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]    |                                                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:88:59
[INFO] [stdout]    |
[INFO] [stdout] 88 |                 + backward_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX)
[INFO] [stdout]    |                                                           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:90:47
[INFO] [stdout]    |
[INFO] [stdout] 90 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]    |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:90:71
[INFO] [stdout]    |
[INFO] [stdout] 90 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]    |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:97:13
[INFO] [stdout]    |
[INFO] [stdout] 97 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]    |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:98:57
[INFO] [stdout]    |
[INFO] [stdout] 98 |             (forward_matrix.get_special(target_idx - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]    |                                                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:99:59
[INFO] [stdout]    |
[INFO] [stdout] 99 |                 + backward_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout]    |                                                           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:101:47
[INFO] [stdout]     |
[INFO] [stdout] 101 |                     .special_transition_score(Profile::SPECIAL_J_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:101:71
[INFO] [stdout]     |
[INFO] [stdout] 101 |                     .special_transition_score(Profile::SPECIAL_J_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:106:50
[INFO] [stdout]     |
[INFO] [stdout] 106 |         posterior_matrix.set_special(target_idx, Profile::SPECIAL_B_IDX, 0.0);
[INFO] [stdout]     |                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:110:13
[INFO] [stdout]     |
[INFO] [stdout] 110 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:111:57
[INFO] [stdout]     |
[INFO] [stdout] 111 |             (forward_matrix.get_special(target_idx - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:112:59
[INFO] [stdout]     |
[INFO] [stdout] 112 |                 + backward_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:114:47
[INFO] [stdout]     |
[INFO] [stdout] 114 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:114:71
[INFO] [stdout]     |
[INFO] [stdout] 114 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:119:65
[INFO] [stdout]     |
[INFO] [stdout] 119 |         denominator += posterior_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX);
[INFO] [stdout]     |                                                                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:120:65
[INFO] [stdout]     |
[INFO] [stdout] 120 |         denominator += posterior_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX);
[INFO] [stdout]     |                                                                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:121:65
[INFO] [stdout]     |
[INFO] [stdout] 121 |         denominator += posterior_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX);
[INFO] [stdout]     |                                                                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:147:13
[INFO] [stdout]     |
[INFO] [stdout] 147 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:148:54
[INFO] [stdout]     |
[INFO] [stdout] 148 |             posterior_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX) * denominator,
[INFO] [stdout]     |                                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:153:13
[INFO] [stdout]     |
[INFO] [stdout] 153 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:154:54
[INFO] [stdout]     |
[INFO] [stdout] 154 |             posterior_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX) * denominator,
[INFO] [stdout]     |                                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:159:13
[INFO] [stdout]     |
[INFO] [stdout] 159 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:160:54
[INFO] [stdout]     |
[INFO] [stdout] 160 |             posterior_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX) * denominator,
[INFO] [stdout]     |                                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated macro `util::max_f32`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/optimal_accuracy_bounded.rs:2:12
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::max_f32;
[INFO] [stdout]   |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/optimal_accuracy_bounded.rs:3:32
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::structs::dp_matrix::DpMatrix;
[INFO] [stdout]   |                                ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/optimal_accuracy_bounded.rs:4:21
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::structs::Profile;
[INFO] [stdout]   |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/optimal_accuracy_bounded.rs:7:15
[INFO] [stdout]   |
[INFO] [stdout] 7 |     profile: &Profile,
[INFO] [stdout]   |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/optimal_accuracy_bounded.rs:8:29
[INFO] [stdout]   |
[INFO] [stdout] 8 |     posterior_matrix: &impl DpMatrix,
[INFO] [stdout]   |                             ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/optimal_accuracy_bounded.rs:9:31
[INFO] [stdout]   |
[INFO] [stdout] 9 |     optimal_matrix: &mut impl DpMatrix,
[INFO] [stdout]   |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:15:61
[INFO] [stdout]    |
[INFO] [stdout] 15 |     optimal_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_N_IDX, 0.0);
[INFO] [stdout]    |                                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:16:61
[INFO] [stdout]    |
[INFO] [stdout] 16 |     optimal_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_B_IDX, 0.0);
[INFO] [stdout]    |                                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:19:9
[INFO] [stdout]    |
[INFO] [stdout] 19 |         Profile::SPECIAL_E_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:24:9
[INFO] [stdout]    |
[INFO] [stdout] 24 |         Profile::SPECIAL_C_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:29:9
[INFO] [stdout]    |
[INFO] [stdout] 29 |         Profile::SPECIAL_J_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:51:48
[INFO] [stdout]    |
[INFO] [stdout] 51 |         optimal_matrix.set_special(target_idx, Profile::SPECIAL_E_IDX, -f32::INFINITY);
[INFO] [stdout]    |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:59:52
[INFO] [stdout]    |
[INFO] [stdout] 59 |                     profile.transition_score_delta(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:62:52
[INFO] [stdout]    |
[INFO] [stdout] 62 |                     profile.transition_score_delta(Profile::INSERT_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:65:52
[INFO] [stdout]    |
[INFO] [stdout] 65 |                     profile.transition_score_delta(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:68:52
[INFO] [stdout]    |
[INFO] [stdout] 68 |                     profile.transition_score_delta(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:69:71
[INFO] [stdout]    |
[INFO] [stdout] 69 |                         * (optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]    |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:76:17
[INFO] [stdout]    |
[INFO] [stdout] 76 |                 Profile::SPECIAL_E_IDX,
[INFO] [stdout]    |                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:78:60
[INFO] [stdout]    |
[INFO] [stdout] 78 |                     optimal_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]    |                                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:87:52
[INFO] [stdout]    |
[INFO] [stdout] 87 |                     profile.transition_score_delta(Profile::MATCH_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:90:52
[INFO] [stdout]    |
[INFO] [stdout] 90 |                     profile.transition_score_delta(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:100:52
[INFO] [stdout]     |
[INFO] [stdout] 100 |                     profile.transition_score_delta(Profile::MATCH_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:102:52
[INFO] [stdout]     |
[INFO] [stdout] 102 |                     profile.transition_score_delta(Profile::DELETE_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:113:21
[INFO] [stdout]     |
[INFO] [stdout] 113 |                     Profile::MATCH_TO_MATCH_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:118:21
[INFO] [stdout]     |
[INFO] [stdout] 118 |                     Profile::INSERT_TO_MATCH_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:123:21
[INFO] [stdout]     |
[INFO] [stdout] 123 |                     Profile::DELETE_TO_MATCH_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:128:21
[INFO] [stdout]     |
[INFO] [stdout] 128 |                     Profile::BEGIN_TO_MATCH_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:130:65
[INFO] [stdout]     |
[INFO] [stdout] 130 |                 ) * (optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                                                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:140:21
[INFO] [stdout]     |
[INFO] [stdout] 140 |                     Profile::MATCH_TO_DELETE_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:144:21
[INFO] [stdout]     |
[INFO] [stdout] 144 |                     Profile::DELETE_TO_DELETE_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:154:13
[INFO] [stdout]     |
[INFO] [stdout] 154 |             Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:156:56
[INFO] [stdout]     |
[INFO] [stdout] 156 |                 optimal_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:164:13
[INFO] [stdout]     |
[INFO] [stdout] 164 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:167:21
[INFO] [stdout]     |
[INFO] [stdout] 167 |                     Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:168:21
[INFO] [stdout]     |
[INFO] [stdout] 168 |                     Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:169:65
[INFO] [stdout]     |
[INFO] [stdout] 169 |                 ) * (optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:170:64
[INFO] [stdout]     |
[INFO] [stdout] 170 |                     + posterior_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)),
[INFO] [stdout]     |                                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:172:21
[INFO] [stdout]     |
[INFO] [stdout] 172 |                     Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:173:21
[INFO] [stdout]     |
[INFO] [stdout] 173 |                     Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:174:60
[INFO] [stdout]     |
[INFO] [stdout] 174 |                 ) * optimal_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:180:13
[INFO] [stdout]     |
[INFO] [stdout] 180 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:183:21
[INFO] [stdout]     |
[INFO] [stdout] 183 |                     Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:184:21
[INFO] [stdout]     |
[INFO] [stdout] 184 |                     Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:185:65
[INFO] [stdout]     |
[INFO] [stdout] 185 |                 ) * (optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:186:64
[INFO] [stdout]     |
[INFO] [stdout] 186 |                     + posterior_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX)),
[INFO] [stdout]     |                                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:188:21
[INFO] [stdout]     |
[INFO] [stdout] 188 |                     Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:189:21
[INFO] [stdout]     |
[INFO] [stdout] 189 |                     Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:190:60
[INFO] [stdout]     |
[INFO] [stdout] 190 |                 ) * optimal_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:196:13
[INFO] [stdout]     |
[INFO] [stdout] 196 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:198:49
[INFO] [stdout]     |
[INFO] [stdout] 198 |                 .special_transition_score_delta(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                                                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:198:73
[INFO] [stdout]     |
[INFO] [stdout] 198 |                 .special_transition_score_delta(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                                                                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:199:63
[INFO] [stdout]     |
[INFO] [stdout] 199 |                 * (optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:200:64
[INFO] [stdout]     |
[INFO] [stdout] 200 |                     + posterior_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX)),
[INFO] [stdout]     |                                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:205:13
[INFO] [stdout]     |
[INFO] [stdout] 205 |             Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:208:21
[INFO] [stdout]     |
[INFO] [stdout] 208 |                     Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:209:21
[INFO] [stdout]     |
[INFO] [stdout] 209 |                     Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:210:60
[INFO] [stdout]     |
[INFO] [stdout] 210 |                 ) * optimal_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX),
[INFO] [stdout]     |                                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:212:21
[INFO] [stdout]     |
[INFO] [stdout] 212 |                     Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:213:21
[INFO] [stdout]     |
[INFO] [stdout] 213 |                     Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:214:60
[INFO] [stdout]     |
[INFO] [stdout] 214 |                 ) * optimal_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated macro `util::log_sum`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/cloud_search_backward.rs:4:12
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::log_sum;
[INFO] [stdout]   |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/cloud_search_backward.rs:5:22
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/cloud_search_backward.rs:5:31
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/cloud_search_backward.rs:6:18
[INFO] [stdout]   |
[INFO] [stdout] 6 | use crate::util::log_add;
[INFO] [stdout]   |                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_backward.rs:10:14
[INFO] [stdout]    |
[INFO] [stdout] 10 |     target: &Sequence,
[INFO] [stdout]    |              ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_backward.rs:11:15
[INFO] [stdout]    |
[INFO] [stdout] 11 |     profile: &Profile,
[INFO] [stdout]    |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/cloud_search_backward.rs:52:9
[INFO] [stdout]     |
[INFO] [stdout]  52 | /         log_sum!(
[INFO] [stdout]  53 | |             cloud_matrix.get_match(match_source_row_idx, profile_idx + 1)
[INFO] [stdout]  54 | |                 + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]  55 | |                 + profile.match_score(previous_target_character, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout]  60 | |                 + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]  61 | |         ),
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_backward.rs:54:44
[INFO] [stdout]    |
[INFO] [stdout] 54 |                 + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/cloud_search_backward.rs:52:9
[INFO] [stdout]     |
[INFO] [stdout]  52 | /         log_sum!(
[INFO] [stdout]  53 | |             cloud_matrix.get_match(match_source_row_idx, profile_idx + 1)
[INFO] [stdout]  54 | |                 + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]  55 | |                 + profile.match_score(previous_target_character, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout]  60 | |                 + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]  61 | |         ),
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_backward.rs:57:44
[INFO] [stdout]    |
[INFO] [stdout] 57 |                 + profile.transition_score(Profile::MATCH_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_backward.rs:60:44
[INFO] [stdout]    |
[INFO] [stdout] 60 |                 + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/cloud_search_backward.rs:73:9
[INFO] [stdout]     |
[INFO] [stdout]  73 | /         log_sum!(
[INFO] [stdout]  74 | |             cloud_matrix.get_match(match_source_row_idx, profile_idx + 1)
[INFO] [stdout]  75 | |                 + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]  76 | |                 + profile.match_score(previous_target_character, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout]  79 | |                 + profile.insert_score(previous_target_character, profile_idx)
[INFO] [stdout]  80 | |         ),
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_backward.rs:75:44
[INFO] [stdout]    |
[INFO] [stdout] 75 |                 + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_backward.rs:78:44
[INFO] [stdout]    |
[INFO] [stdout] 78 |                 + profile.transition_score(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/cloud_search_backward.rs:92:9
[INFO] [stdout]     |
[INFO] [stdout]  92 | /         log_sum!(
[INFO] [stdout]  93 | |             cloud_matrix.get_match(match_source_row_idx, profile_idx + 1)
[INFO] [stdout]  94 | |                 + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]  95 | |                 + profile.match_score(previous_target_character, profile_idx + 1),
[INFO] [stdout]  96 | |             cloud_matrix.get_delete(delete_source_row_idx, profile_idx + 1)
[INFO] [stdout]  97 | |                 + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]  98 | |         ),
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_backward.rs:94:44
[INFO] [stdout]    |
[INFO] [stdout] 94 |                 + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_backward.rs:97:44
[INFO] [stdout]    |
[INFO] [stdout] 97 |                 + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/cloud_search_backward.rs:103:15
[INFO] [stdout]     |
[INFO] [stdout] 103 |     profile: &Profile,
[INFO] [stdout]     |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/cloud_search_backward.rs:104:14
[INFO] [stdout]     |
[INFO] [stdout] 104 |     target: &Sequence,
[INFO] [stdout]     |              ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated macro `util::log_sum`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/cloud_search_forward.rs:3:12
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::log_sum;
[INFO] [stdout]   |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/cloud_search_forward.rs:4:22
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/cloud_search_forward.rs:4:31
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/cloud_search_forward.rs:5:18
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::util::log_add;
[INFO] [stdout]   |                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/cloud_search_forward.rs:9:14
[INFO] [stdout]   |
[INFO] [stdout] 9 |     target: &Sequence,
[INFO] [stdout]   |              ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_forward.rs:10:15
[INFO] [stdout]    |
[INFO] [stdout] 10 |     profile: &Profile,
[INFO] [stdout]    |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/cloud_search_forward.rs:43:9
[INFO] [stdout]     |
[INFO] [stdout]  43 | /         log_sum!(
[INFO] [stdout]  44 | |             cloud_matrix.get_match(source_row_idx, source_profile_idx)
[INFO] [stdout]  45 | |                 + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, source_profile_idx),
[INFO] [stdout]  46 | |             cloud_matrix.get_insert(source_row_idx, source_profile_idx)
[INFO] [stdout] ...   |
[INFO] [stdout]  49 | |                 + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, source_profile_idx)
[INFO] [stdout]  50 | |         ) + profile.match_score(current_target_character as usize, profile_idx),
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_forward.rs:45:44
[INFO] [stdout]    |
[INFO] [stdout] 45 |                 + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, source_profile_idx),
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/cloud_search_forward.rs:43:9
[INFO] [stdout]     |
[INFO] [stdout]  43 | /         log_sum!(
[INFO] [stdout]  44 | |             cloud_matrix.get_match(source_row_idx, source_profile_idx)
[INFO] [stdout]  45 | |                 + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, source_profile_idx),
[INFO] [stdout]  46 | |             cloud_matrix.get_insert(source_row_idx, source_profile_idx)
[INFO] [stdout] ...   |
[INFO] [stdout]  49 | |                 + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, source_profile_idx)
[INFO] [stdout]  50 | |         ) + profile.match_score(current_target_character as usize, profile_idx),
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_forward.rs:47:44
[INFO] [stdout]    |
[INFO] [stdout] 47 |                 + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, source_profile_idx),
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_forward.rs:49:44
[INFO] [stdout]    |
[INFO] [stdout] 49 |                 + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, source_profile_idx)
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/cloud_search_forward.rs:64:9
[INFO] [stdout]     |
[INFO] [stdout]  64 | /         log_sum!(
[INFO] [stdout]  65 | |             cloud_matrix.get_match(source_row_idx, profile_idx)
[INFO] [stdout]  66 | |                 + profile.transition_score(Profile::MATCH_TO_INSERT_IDX, profile_idx),
[INFO] [stdout]  67 | |             cloud_matrix.get_insert(source_row_idx, profile_idx)
[INFO] [stdout]  68 | |                 + profile.transition_score(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]  69 | |         ) + profile.insert_score(current_target_character as usize, profile_idx),
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_forward.rs:66:44
[INFO] [stdout]    |
[INFO] [stdout] 66 |                 + profile.transition_score(Profile::MATCH_TO_INSERT_IDX, profile_idx),
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_forward.rs:68:44
[INFO] [stdout]    |
[INFO] [stdout] 68 |                 + profile.transition_score(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/cloud_search_forward.rs:83:9
[INFO] [stdout]     |
[INFO] [stdout]  83 | /         log_sum!(
[INFO] [stdout]  84 | |             cloud_matrix.get_match(source_row_idx, source_profile_idx)
[INFO] [stdout]  85 | |                 + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, source_profile_idx),
[INFO] [stdout]  86 | |             cloud_matrix.get_delete(source_row_idx, source_profile_idx)
[INFO] [stdout]  87 | |                 + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, source_profile_idx)
[INFO] [stdout]  88 | |         ),
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_forward.rs:85:44
[INFO] [stdout]    |
[INFO] [stdout] 85 |                 + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, source_profile_idx),
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_forward.rs:87:44
[INFO] [stdout]    |
[INFO] [stdout] 87 |                 + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, source_profile_idx)
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_forward.rs:93:15
[INFO] [stdout]    |
[INFO] [stdout] 93 |     profile: &Profile,
[INFO] [stdout]    |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/cloud_search_forward.rs:94:14
[INFO] [stdout]    |
[INFO] [stdout] 94 |     target: &Sequence,
[INFO] [stdout]    |              ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated macro `util::log_sum`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/scoring.rs:2:12
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::log_sum;
[INFO] [stdout]   |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/scoring.rs:3:32
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::structs::dp_matrix::DpMatrix;
[INFO] [stdout]   |                                ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/scoring.rs:4:22
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/scoring.rs:4:31
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/scoring.rs:5:19
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::util::{log_add, LogAbuse};
[INFO] [stdout]   |                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `util::LogAbuse`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/scoring.rs:5:28
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::util::{log_add, LogAbuse};
[INFO] [stdout]   |                            ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/scoring.rs:14:15
[INFO] [stdout]    |
[INFO] [stdout] 14 |     profile: &Profile,
[INFO] [stdout]    |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/scoring.rs:15:14
[INFO] [stdout]    |
[INFO] [stdout] 15 |     target: &Sequence,
[INFO] [stdout]    |              ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/scoring.rs:13:29
[INFO] [stdout]    |
[INFO] [stdout] 13 |     posterior_matrix: &impl DpMatrix,
[INFO] [stdout]    |                             ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/scoring.rs:42:61
[INFO] [stdout]    |
[INFO] [stdout] 42 |         n_value += posterior_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX);
[INFO] [stdout]    |                                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/scoring.rs:43:61
[INFO] [stdout]    |
[INFO] [stdout] 43 |         j_value += posterior_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX);
[INFO] [stdout]    |                                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/scoring.rs:44:61
[INFO] [stdout]    |
[INFO] [stdout] 44 |         c_value += posterior_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX);
[INFO] [stdout]    |                                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/scoring.rs:66:52
[INFO] [stdout]    |
[INFO] [stdout] 66 |     let mut null2: Vec<f32> = vec![-f32::INFINITY; Profile::MAX_DEGENERATE_ALPHABET_SIZE];
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |         log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/scoring.rs:67:20
[INFO] [stdout]     |
[INFO] [stdout]  67 |     let x_factor = log_sum!(n_value, j_value, c_value);
[INFO] [stdout]     |                    ----------------------------------- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |         log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/scoring.rs:67:20
[INFO] [stdout]     |
[INFO] [stdout]  67 |     let x_factor = log_sum!(n_value, j_value, c_value);
[INFO] [stdout]     |                    ----------------------------------- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/scoring.rs:69:28
[INFO] [stdout]    |
[INFO] [stdout] 69 |     for alphabet_idx in 0..Profile::MAX_ALPHABET_SIZE {
[INFO] [stdout]    |                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/scoring.rs:71:35
[INFO] [stdout]     |
[INFO] [stdout]  71 |               null2[alphabet_idx] = log_sum!(
[INFO] [stdout]     |  ___________________________________-
[INFO] [stdout]  72 | |                 null2[alphabet_idx],
[INFO] [stdout]  73 | |                 match_values[profile_idx] + profile.match_score(alphabet_idx, profile_idx),
[INFO] [stdout]  74 | |                 insert_values[profile_idx] + profile.insert_score(alphabet_idx, profile_idx)
[INFO] [stdout]  75 | |             );
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/scoring.rs:71:35
[INFO] [stdout]     |
[INFO] [stdout]  71 |               null2[alphabet_idx] = log_sum!(
[INFO] [stdout]     |  ___________________________________-
[INFO] [stdout]  72 | |                 null2[alphabet_idx],
[INFO] [stdout]  73 | |                 match_values[profile_idx] + profile.match_score(alphabet_idx, profile_idx),
[INFO] [stdout]  74 | |                 insert_values[profile_idx] + profile.insert_score(alphabet_idx, profile_idx)
[INFO] [stdout]  75 | |             );
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/scoring.rs:77:31
[INFO] [stdout]     |
[INFO] [stdout]  77 |           null2[alphabet_idx] = log_sum!(
[INFO] [stdout]     |  _______________________________-
[INFO] [stdout]  78 | |             null2[alphabet_idx],
[INFO] [stdout]  79 | |             match_values[profile.length] + profile.match_score(alphabet_idx, profile.length),
[INFO] [stdout]  80 | |             x_factor
[INFO] [stdout]  81 | |         );
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/scoring.rs:77:31
[INFO] [stdout]     |
[INFO] [stdout]  77 |           null2[alphabet_idx] = log_sum!(
[INFO] [stdout]     |  _______________________________-
[INFO] [stdout]  78 | |             null2[alphabet_idx],
[INFO] [stdout]  79 | |             match_values[profile.length] + profile.match_score(alphabet_idx, profile.length),
[INFO] [stdout]  80 | |             x_factor
[INFO] [stdout]  81 | |         );
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/scoring.rs:116:11
[INFO] [stdout]     |
[INFO] [stdout] 116 |     null2[Profile::GAP_INDEX] = 1.0;
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/scoring.rs:117:11
[INFO] [stdout]     |
[INFO] [stdout] 117 |     null2[Profile::NON_RESIDUE_IDX] = 1.0;
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/scoring.rs:118:11
[INFO] [stdout]     |
[INFO] [stdout] 118 |     null2[Profile::MISSING_DATA_IDX] = 1.0;
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |         log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/bounded/scoring.rs:129:19
[INFO] [stdout]     |
[INFO] [stdout] 129 |     null2_score = log_sum!(0.0, null2_prior + null2_score);
[INFO] [stdout]     |                   ---------------------------------------- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:1:32
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::structs::dp_matrix::DpMatrix;
[INFO] [stdout]   |                                ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_B`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 |     TRACE_B, TRACE_C, TRACE_D, TRACE_E, TRACE_I, TRACE_J, TRACE_M, TRACE_N, TRACE_S, TRACE_T,
[INFO] [stdout]   |     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_C`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:3:14
[INFO] [stdout]   |
[INFO] [stdout] 3 |     TRACE_B, TRACE_C, TRACE_D, TRACE_E, TRACE_I, TRACE_J, TRACE_M, TRACE_N, TRACE_S, TRACE_T,
[INFO] [stdout]   |              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_D`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:3:23
[INFO] [stdout]   |
[INFO] [stdout] 3 |     TRACE_B, TRACE_C, TRACE_D, TRACE_E, TRACE_I, TRACE_J, TRACE_M, TRACE_N, TRACE_S, TRACE_T,
[INFO] [stdout]   |                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_E`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:3:32
[INFO] [stdout]   |
[INFO] [stdout] 3 |     TRACE_B, TRACE_C, TRACE_D, TRACE_E, TRACE_I, TRACE_J, TRACE_M, TRACE_N, TRACE_S, TRACE_T,
[INFO] [stdout]   |                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_I`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:3:41
[INFO] [stdout]   |
[INFO] [stdout] 3 |     TRACE_B, TRACE_C, TRACE_D, TRACE_E, TRACE_I, TRACE_J, TRACE_M, TRACE_N, TRACE_S, TRACE_T,
[INFO] [stdout]   |                                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_J`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:3:50
[INFO] [stdout]   |
[INFO] [stdout] 3 |     TRACE_B, TRACE_C, TRACE_D, TRACE_E, TRACE_I, TRACE_J, TRACE_M, TRACE_N, TRACE_S, TRACE_T,
[INFO] [stdout]   |                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_M`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:3:59
[INFO] [stdout]   |
[INFO] [stdout] 3 |     TRACE_B, TRACE_C, TRACE_D, TRACE_E, TRACE_I, TRACE_J, TRACE_M, TRACE_N, TRACE_S, TRACE_T,
[INFO] [stdout]   |                                                           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_N`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:3:68
[INFO] [stdout]   |
[INFO] [stdout] 3 |     TRACE_B, TRACE_C, TRACE_D, TRACE_E, TRACE_I, TRACE_J, TRACE_M, TRACE_N, TRACE_S, TRACE_T,
[INFO] [stdout]   |                                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_S`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:3:77
[INFO] [stdout]   |
[INFO] [stdout] 3 |     TRACE_B, TRACE_C, TRACE_D, TRACE_E, TRACE_I, TRACE_J, TRACE_M, TRACE_N, TRACE_S, TRACE_T,
[INFO] [stdout]   |                                                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_T`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:3:86
[INFO] [stdout]   |
[INFO] [stdout] 3 |     TRACE_B, TRACE_C, TRACE_D, TRACE_E, TRACE_I, TRACE_J, TRACE_M, TRACE_N, TRACE_S, TRACE_T,
[INFO] [stdout]   |                                                                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:5:22
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::structs::{Profile, Trace};
[INFO] [stdout]   |                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::trace::Trace`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:5:31
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::structs::{Profile, Trace};
[INFO] [stdout]   |                               ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:8:15
[INFO] [stdout]   |
[INFO] [stdout] 8 |     profile: &Profile,
[INFO] [stdout]   |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::trace::Trace`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:11:17
[INFO] [stdout]    |
[INFO] [stdout] 11 |     trace: &mut Trace,
[INFO] [stdout]    |                 ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/bounded/traceback_bounded.rs:9:29
[INFO] [stdout]   |
[INFO] [stdout] 9 |     posterior_matrix: &impl DpMatrix,
[INFO] [stdout]   |                             ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:10:27
[INFO] [stdout]    |
[INFO] [stdout] 10 |     optimal_matrix: &impl DpMatrix,
[INFO] [stdout]    |                           ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_C`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:19:37
[INFO] [stdout]    |
[INFO] [stdout] 19 |     let mut previous_state: usize = TRACE_C;
[INFO] [stdout]    |                                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_T`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:22:45
[INFO] [stdout]    |
[INFO] [stdout] 22 |     trace.append_with_posterior_probability(TRACE_T, target_idx, profile_idx, 0.0);
[INFO] [stdout]    |                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_C`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:23:45
[INFO] [stdout]    |
[INFO] [stdout] 23 |     trace.append_with_posterior_probability(TRACE_C, target_idx, profile_idx, 0.0);
[INFO] [stdout]    |                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_S`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:25:29
[INFO] [stdout]    |
[INFO] [stdout] 25 |     while previous_state != TRACE_S {
[INFO] [stdout]    |                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_C`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:27:13
[INFO] [stdout]    |
[INFO] [stdout] 27 |             TRACE_C => {
[INFO] [stdout]    |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:29:21
[INFO] [stdout]    |
[INFO] [stdout] 29 |                     Profile::SPECIAL_C_IDX,
[INFO] [stdout]    |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:30:21
[INFO] [stdout]    |
[INFO] [stdout] 30 |                     Profile::SPECIAL_LOOP_IDX,
[INFO] [stdout]    |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:32:50
[INFO] [stdout]    |
[INFO] [stdout] 32 |                     .get_special(target_idx - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]    |                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:34:64
[INFO] [stdout]    |
[INFO] [stdout] 34 |                     + posterior_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX));
[INFO] [stdout]    |                                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:37:45
[INFO] [stdout]    |
[INFO] [stdout] 37 |                     .transition_score_delta(Profile::SPECIAL_E_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]    |                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:37:69
[INFO] [stdout]    |
[INFO] [stdout] 37 |                     .transition_score_delta(Profile::SPECIAL_E_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]    |                                                                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:38:62
[INFO] [stdout]    |
[INFO] [stdout] 38 |                     * optimal_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX);
[INFO] [stdout]    |                                                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_C`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:41:21
[INFO] [stdout]    |
[INFO] [stdout] 41 |                     TRACE_C
[INFO] [stdout]    |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_E`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:43:21
[INFO] [stdout]    |
[INFO] [stdout] 43 |                     TRACE_E
[INFO] [stdout]    |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_E`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:46:13
[INFO] [stdout]    |
[INFO] [stdout] 46 |             TRACE_E => {
[INFO] [stdout]    |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_M`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:56:46
[INFO] [stdout]    |
[INFO] [stdout] 56 |                         state_of_max_score = TRACE_M;
[INFO] [stdout]    |                                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_D`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:61:46
[INFO] [stdout]    |
[INFO] [stdout] 61 |                         state_of_max_score = TRACE_D;
[INFO] [stdout]    |                                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_M`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:68:13
[INFO] [stdout]    |
[INFO] [stdout] 68 |             TRACE_M => {
[INFO] [stdout]    |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_M`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:69:52
[INFO] [stdout]    |
[INFO] [stdout] 69 |                 let possible_states: [usize; 4] = [TRACE_M, TRACE_I, TRACE_D, TRACE_B];
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_I`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:69:61
[INFO] [stdout]    |
[INFO] [stdout] 69 |                 let possible_states: [usize; 4] = [TRACE_M, TRACE_I, TRACE_D, TRACE_B];
[INFO] [stdout]    |                                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_D`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:69:70
[INFO] [stdout]    |
[INFO] [stdout] 69 |                 let possible_states: [usize; 4] = [TRACE_M, TRACE_I, TRACE_D, TRACE_B];
[INFO] [stdout]    |                                                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_B`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:69:79
[INFO] [stdout]    |
[INFO] [stdout] 69 |                 let possible_states: [usize; 4] = [TRACE_M, TRACE_I, TRACE_D, TRACE_B];
[INFO] [stdout]    |                                                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:72:52
[INFO] [stdout]    |
[INFO] [stdout] 72 |                     profile.transition_score_delta(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:74:52
[INFO] [stdout]    |
[INFO] [stdout] 74 |                     profile.transition_score_delta(Profile::INSERT_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:76:52
[INFO] [stdout]    |
[INFO] [stdout] 76 |                     profile.transition_score_delta(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:78:52
[INFO] [stdout]    |
[INFO] [stdout] 78 |                     profile.transition_score_delta(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:79:70
[INFO] [stdout]    |
[INFO] [stdout] 79 |                         * optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX),
[INFO] [stdout]    |                                                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_I`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:95:13
[INFO] [stdout]    |
[INFO] [stdout] 95 |             TRACE_I => {
[INFO] [stdout]    |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/traceback_bounded.rs:97:45
[INFO] [stdout]    |
[INFO] [stdout] 97 |                     .transition_score_delta(Profile::MATCH_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:101:45
[INFO] [stdout]     |
[INFO] [stdout] 101 |                     .transition_score_delta(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]     |                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_M`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:108:21
[INFO] [stdout]     |
[INFO] [stdout] 108 |                     TRACE_M
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_I`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:110:21
[INFO] [stdout]     |
[INFO] [stdout] 110 |                     TRACE_I
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_D`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:113:13
[INFO] [stdout]     |
[INFO] [stdout] 113 |             TRACE_D => {
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:115:45
[INFO] [stdout]     |
[INFO] [stdout] 115 |                     .transition_score_delta(Profile::MATCH_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]     |                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:119:45
[INFO] [stdout]     |
[INFO] [stdout] 119 |                     .transition_score_delta(Profile::DELETE_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]     |                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_M`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:126:21
[INFO] [stdout]     |
[INFO] [stdout] 126 |                     TRACE_M
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_D`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:128:21
[INFO] [stdout]     |
[INFO] [stdout] 128 |                     TRACE_D
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_B`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:131:13
[INFO] [stdout]     |
[INFO] [stdout] 131 |             TRACE_B => {
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:133:21
[INFO] [stdout]     |
[INFO] [stdout] 133 |                     Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:134:21
[INFO] [stdout]     |
[INFO] [stdout] 134 |                     Profile::SPECIAL_MOVE_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:136:46
[INFO] [stdout]     |
[INFO] [stdout] 136 |                     .get_special(target_idx, Profile::SPECIAL_N_IDX);
[INFO] [stdout]     |                                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:139:21
[INFO] [stdout]     |
[INFO] [stdout] 139 |                     Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:140:21
[INFO] [stdout]     |
[INFO] [stdout] 140 |                     Profile::SPECIAL_MOVE_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:142:46
[INFO] [stdout]     |
[INFO] [stdout] 142 |                     .get_special(target_idx, Profile::SPECIAL_J_IDX);
[INFO] [stdout]     |                                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_N`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:145:21
[INFO] [stdout]     |
[INFO] [stdout] 145 |                     TRACE_N
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_J`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:147:21
[INFO] [stdout]     |
[INFO] [stdout] 147 |                     TRACE_J
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_N`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:150:13
[INFO] [stdout]     |
[INFO] [stdout] 150 |             TRACE_N => {
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_S`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:152:21
[INFO] [stdout]     |
[INFO] [stdout] 152 |                     TRACE_S
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_N`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:154:21
[INFO] [stdout]     |
[INFO] [stdout] 154 |                     TRACE_N
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_J`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:157:13
[INFO] [stdout]     |
[INFO] [stdout] 157 |             TRACE_J => {
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:159:21
[INFO] [stdout]     |
[INFO] [stdout] 159 |                     Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:160:21
[INFO] [stdout]     |
[INFO] [stdout] 160 |                     Profile::SPECIAL_LOOP_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:162:50
[INFO] [stdout]     |
[INFO] [stdout] 162 |                     .get_special(target_idx - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:164:64
[INFO] [stdout]     |
[INFO] [stdout] 164 |                     + posterior_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX));
[INFO] [stdout]     |                                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:167:21
[INFO] [stdout]     |
[INFO] [stdout] 167 |                     Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:168:21
[INFO] [stdout]     |
[INFO] [stdout] 168 |                     Profile::SPECIAL_LOOP_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:170:46
[INFO] [stdout]     |
[INFO] [stdout] 170 |                     .get_special(target_idx, Profile::SPECIAL_E_IDX);
[INFO] [stdout]     |                                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_J`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:173:21
[INFO] [stdout]     |
[INFO] [stdout] 173 |                     TRACE_J
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_E`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:175:21
[INFO] [stdout]     |
[INFO] [stdout] 175 |                     TRACE_E
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_N`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:198:30
[INFO] [stdout]     |
[INFO] [stdout] 198 |         if (current_state == TRACE_N || current_state == TRACE_J || current_state == TRACE_C)
[INFO] [stdout]     |                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_J`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:198:58
[INFO] [stdout]     |
[INFO] [stdout] 198 |         if (current_state == TRACE_N || current_state == TRACE_J || current_state == TRACE_C)
[INFO] [stdout]     |                                                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_C`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:198:86
[INFO] [stdout]     |
[INFO] [stdout] 198 |         if (current_state == TRACE_N || current_state == TRACE_J || current_state == TRACE_C)
[INFO] [stdout]     |                                                                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:209:27
[INFO] [stdout]     |
[INFO] [stdout] 209 |     optimal_matrix: &impl DpMatrix,
[INFO] [stdout]     |                           ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_M`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:216:9
[INFO] [stdout]     |
[INFO] [stdout] 216 |         TRACE_M => optimal_matrix.get_match(target_idx, profile_idx),
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_I`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:217:9
[INFO] [stdout]     |
[INFO] [stdout] 217 |         TRACE_I => optimal_matrix.get_insert(target_idx, profile_idx),
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_N`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:218:9
[INFO] [stdout]     |
[INFO] [stdout] 218 |         TRACE_N => {
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:220:56
[INFO] [stdout]     |
[INFO] [stdout] 220 |                 optimal_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_C`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:225:9
[INFO] [stdout]     |
[INFO] [stdout] 225 |         TRACE_C => {
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:227:56
[INFO] [stdout]     |
[INFO] [stdout] 227 |                 optimal_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `structs::trace::constants::TRACE_J`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:232:9
[INFO] [stdout]     |
[INFO] [stdout] 232 |         TRACE_J => {
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/traceback_bounded.rs:234:56
[INFO] [stdout]     |
[INFO] [stdout] 234 |                 optimal_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated macro `util::log_sum`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/backward.rs:1:12
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::log_sum;
[INFO] [stdout]   |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/backward.rs:2:32
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::structs::dp_matrix::DpMatrix;
[INFO] [stdout]   |                                ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/backward.rs:3:22
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/backward.rs:3:31
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/backward.rs:4:18
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::util::log_add;
[INFO] [stdout]   |                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/backward.rs:6:27
[INFO] [stdout]   |
[INFO] [stdout] 6 | pub fn backward(profile: &Profile, target: &Sequence, dp_matrix: &mut impl DpMatrix) {
[INFO] [stdout]   |                           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/backward.rs:6:45
[INFO] [stdout]   |
[INFO] [stdout] 6 | pub fn backward(profile: &Profile, target: &Sequence, dp_matrix: &mut impl DpMatrix) {
[INFO] [stdout]   |                                             ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/backward.rs:6:76
[INFO] [stdout]   |
[INFO] [stdout] 6 | pub fn backward(profile: &Profile, target: &Sequence, dp_matrix: &mut impl DpMatrix) {
[INFO] [stdout]   |                                                                            ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:10:42
[INFO] [stdout]    |
[INFO] [stdout] 10 |     dp_matrix.set_special(target.length, Profile::SPECIAL_J_IDX, -f32::INFINITY);
[INFO] [stdout]    |                                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:11:42
[INFO] [stdout]    |
[INFO] [stdout] 11 |     dp_matrix.set_special(target.length, Profile::SPECIAL_B_IDX, -f32::INFINITY);
[INFO] [stdout]    |                                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:12:42
[INFO] [stdout]    |
[INFO] [stdout] 12 |     dp_matrix.set_special(target.length, Profile::SPECIAL_N_IDX, -f32::INFINITY);
[INFO] [stdout]    |                                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:15:9
[INFO] [stdout]    |
[INFO] [stdout] 15 |         Profile::SPECIAL_C_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:16:42
[INFO] [stdout]    |
[INFO] [stdout] 16 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:16:66
[INFO] [stdout]    |
[INFO] [stdout] 16 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:21:9
[INFO] [stdout]    |
[INFO] [stdout] 21 |         Profile::SPECIAL_E_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:22:42
[INFO] [stdout]    |
[INFO] [stdout] 22 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]    |                                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:22:66
[INFO] [stdout]    |
[INFO] [stdout] 22 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]    |                                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:23:48
[INFO] [stdout]    |
[INFO] [stdout] 23 |             + profile.special_transition_score(Profile::SPECIAL_E_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:23:72
[INFO] [stdout]    |
[INFO] [stdout] 23 |             + profile.special_transition_score(Profile::SPECIAL_E_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:29:46
[INFO] [stdout]    |
[INFO] [stdout] 29 |         dp_matrix.get_special(target.length, Profile::SPECIAL_E_IDX),
[INFO] [stdout]    |                                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:35:46
[INFO] [stdout]    |
[INFO] [stdout] 35 |         dp_matrix.get_special(target.length, Profile::SPECIAL_E_IDX),
[INFO] [stdout]    |                                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:44:13
[INFO] [stdout]     |
[INFO] [stdout]  44 | /             log_sum!(
[INFO] [stdout]  45 | |                 dp_matrix.get_special(target.length, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]  46 | |                 dp_matrix.get_delete(target.length, profile_idx + 1)
[INFO] [stdout]  47 | |                     + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]  48 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:45:54
[INFO] [stdout]    |
[INFO] [stdout] 45 |                 dp_matrix.get_special(target.length, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]    |                                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:47:48
[INFO] [stdout]    |
[INFO] [stdout] 47 |                     + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]    |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:55:13
[INFO] [stdout]     |
[INFO] [stdout]  55 | /             log_sum!(
[INFO] [stdout]  56 | |                 dp_matrix.get_special(target.length, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]  57 | |                 dp_matrix.get_delete(target.length, profile_idx + 1)
[INFO] [stdout]  58 | |                     + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]  59 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:56:54
[INFO] [stdout]    |
[INFO] [stdout] 56 |                 dp_matrix.get_special(target.length, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]    |                                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:58:48
[INFO] [stdout]    |
[INFO] [stdout] 58 |                     + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]    |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:68:13
[INFO] [stdout]    |
[INFO] [stdout] 68 |             Profile::SPECIAL_B_IDX,
[INFO] [stdout]    |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:70:44
[INFO] [stdout]    |
[INFO] [stdout] 70 |                 + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, 0)
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:79:17
[INFO] [stdout]    |
[INFO] [stdout] 79 |                 Profile::SPECIAL_B_IDX,
[INFO] [stdout]    |                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:80:17
[INFO] [stdout]     |
[INFO] [stdout]  80 | /                 log_sum!(
[INFO] [stdout]  81 | |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX),
[INFO] [stdout]  82 | |                     dp_matrix.get_match(target_idx + 1, profile_idx)
[INFO] [stdout]  83 | |                         + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]  84 | |                         + profile.match_score(current_residue, profile_idx)
[INFO] [stdout]  85 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:81:55
[INFO] [stdout]    |
[INFO] [stdout] 81 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX),
[INFO] [stdout]    |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:83:52
[INFO] [stdout]    |
[INFO] [stdout] 83 |                         + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:91:13
[INFO] [stdout]    |
[INFO] [stdout] 91 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]    |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:92:13
[INFO] [stdout]     |
[INFO] [stdout]  92 | /             log_sum!(
[INFO] [stdout]  93 | |                 dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]  94 | |                     + profile.special_transition_score(
[INFO] [stdout]  95 | |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout] ...   |
[INFO] [stdout] 103 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:93:55
[INFO] [stdout]    |
[INFO] [stdout] 93 |                 dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]    |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:95:25
[INFO] [stdout]    |
[INFO] [stdout] 95 |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout]    |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:96:25
[INFO] [stdout]    |
[INFO] [stdout] 96 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]    |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/backward.rs:98:51
[INFO] [stdout]    |
[INFO] [stdout] 98 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX)
[INFO] [stdout]    |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:100:25
[INFO] [stdout]     |
[INFO] [stdout] 100 |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:101:25
[INFO] [stdout]     |
[INFO] [stdout] 101 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:108:13
[INFO] [stdout]     |
[INFO] [stdout] 108 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:109:51
[INFO] [stdout]     |
[INFO] [stdout] 109 |             dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:111:47
[INFO] [stdout]     |
[INFO] [stdout] 111 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:111:71
[INFO] [stdout]     |
[INFO] [stdout] 111 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:116:13
[INFO] [stdout]     |
[INFO] [stdout] 116 |             Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:117:13
[INFO] [stdout]     |
[INFO] [stdout] 117 | /             log_sum!(
[INFO] [stdout] 118 | |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout] 119 | |                     + profile.special_transition_score(
[INFO] [stdout] 120 | |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout] ...   |
[INFO] [stdout] 128 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:118:51
[INFO] [stdout]     |
[INFO] [stdout] 118 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:120:25
[INFO] [stdout]     |
[INFO] [stdout] 120 |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:121:25
[INFO] [stdout]     |
[INFO] [stdout] 121 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:123:51
[INFO] [stdout]     |
[INFO] [stdout] 123 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:125:25
[INFO] [stdout]     |
[INFO] [stdout] 125 |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:126:25
[INFO] [stdout]     |
[INFO] [stdout] 126 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:133:13
[INFO] [stdout]     |
[INFO] [stdout] 133 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:134:13
[INFO] [stdout]     |
[INFO] [stdout] 134 | /             log_sum!(
[INFO] [stdout] 135 | |                 dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout] 136 | |                     + profile.special_transition_score(
[INFO] [stdout] 137 | |                         Profile::SPECIAL_N_IDX,
[INFO] [stdout] ...   |
[INFO] [stdout] 145 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:135:55
[INFO] [stdout]     |
[INFO] [stdout] 135 |                 dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:137:25
[INFO] [stdout]     |
[INFO] [stdout] 137 |                         Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:138:25
[INFO] [stdout]     |
[INFO] [stdout] 138 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:140:51
[INFO] [stdout]     |
[INFO] [stdout] 140 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:142:25
[INFO] [stdout]     |
[INFO] [stdout] 142 |                         Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:143:25
[INFO] [stdout]     |
[INFO] [stdout] 143 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:151:47
[INFO] [stdout]     |
[INFO] [stdout] 151 |             dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:159:47
[INFO] [stdout]     |
[INFO] [stdout] 159 |             dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:166:17
[INFO] [stdout]     |
[INFO] [stdout] 166 | /                 log_sum!(
[INFO] [stdout] 167 | |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout] 168 | |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx)
[INFO] [stdout] 169 | |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout] 175 | |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout] 176 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:168:52
[INFO] [stdout]     |
[INFO] [stdout] 168 |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:166:17
[INFO] [stdout]     |
[INFO] [stdout] 166 | /                 log_sum!(
[INFO] [stdout] 167 | |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout] 168 | |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx)
[INFO] [stdout] 169 | |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout] 175 | |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout] 176 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:171:52
[INFO] [stdout]     |
[INFO] [stdout] 171 |                         + profile.transition_score(Profile::MATCH_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:166:17
[INFO] [stdout]     |
[INFO] [stdout] 166 | /                 log_sum!(
[INFO] [stdout] 167 | |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout] 168 | |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx)
[INFO] [stdout] 169 | |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout] 175 | |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout] 176 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:173:55
[INFO] [stdout]     |
[INFO] [stdout] 173 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:175:52
[INFO] [stdout]     |
[INFO] [stdout] 175 |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:182:17
[INFO] [stdout]     |
[INFO] [stdout] 182 | /                 log_sum!(
[INFO] [stdout] 183 | |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout] 184 | |                         + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, profile_idx)
[INFO] [stdout] 185 | |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout] 188 | |                         + profile.insert_score(current_residue, profile_idx)
[INFO] [stdout] 189 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:184:52
[INFO] [stdout]     |
[INFO] [stdout] 184 |                         + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:187:52
[INFO] [stdout]     |
[INFO] [stdout] 187 |                         + profile.transition_score(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:195:17
[INFO] [stdout]     |
[INFO] [stdout] 195 | /                 log_sum!(
[INFO] [stdout] 196 | |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout] 197 | |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx)
[INFO] [stdout] 198 | |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout] 201 | |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX) + end_score
[INFO] [stdout] 202 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:197:52
[INFO] [stdout]     |
[INFO] [stdout] 197 |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:195:17
[INFO] [stdout]     |
[INFO] [stdout] 195 | /                 log_sum!(
[INFO] [stdout] 196 | |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout] 197 | |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx)
[INFO] [stdout] 198 | |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout] ...   |
[INFO] [stdout] 201 | |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX) + end_score
[INFO] [stdout] 202 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:200:52
[INFO] [stdout]     |
[INFO] [stdout] 200 |                         + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx),
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:201:55
[INFO] [stdout]     |
[INFO] [stdout] 201 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX) + end_score
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:211:9
[INFO] [stdout]     |
[INFO] [stdout] 211 |         Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:213:40
[INFO] [stdout]     |
[INFO] [stdout] 213 |             + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, 0)
[INFO] [stdout]     |                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:220:13
[INFO] [stdout]     |
[INFO] [stdout] 220 |             Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:221:13
[INFO] [stdout]     |
[INFO] [stdout] 221 | /             log_sum!(
[INFO] [stdout] 222 | |                 dp_matrix.get_special(0, Profile::SPECIAL_B_IDX),
[INFO] [stdout] 223 | |                 dp_matrix.get_match(1, profile_idx)
[INFO] [stdout] 224 | |                     + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout] 225 | |                     + profile.match_score(first_residue, profile_idx)
[INFO] [stdout] 226 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:222:42
[INFO] [stdout]     |
[INFO] [stdout] 222 |                 dp_matrix.get_special(0, Profile::SPECIAL_B_IDX),
[INFO] [stdout]     |                                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:224:48
[INFO] [stdout]     |
[INFO] [stdout] 224 |                     + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:230:30
[INFO] [stdout]     |
[INFO] [stdout] 230 |     dp_matrix.set_special(0, Profile::SPECIAL_J_IDX, -f32::INFINITY);
[INFO] [stdout]     |                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:231:30
[INFO] [stdout]     |
[INFO] [stdout] 231 |     dp_matrix.set_special(0, Profile::SPECIAL_C_IDX, -f32::INFINITY);
[INFO] [stdout]     |                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:232:30
[INFO] [stdout]     |
[INFO] [stdout] 232 |     dp_matrix.set_special(0, Profile::SPECIAL_E_IDX, -f32::INFINITY);
[INFO] [stdout]     |                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:235:9
[INFO] [stdout]     |
[INFO] [stdout] 235 |         Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/backward.rs:236:9
[INFO] [stdout]     |
[INFO] [stdout] 236 | /         log_sum!(
[INFO] [stdout] 237 | |             dp_matrix.get_special(1, Profile::SPECIAL_N_IDX)
[INFO] [stdout] 238 | |                 + profile
[INFO] [stdout] 239 | |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout] ...   |
[INFO] [stdout] 242 | |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout] 243 | |         ),
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:237:38
[INFO] [stdout]     |
[INFO] [stdout] 237 |             dp_matrix.get_special(1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:239:47
[INFO] [stdout]     |
[INFO] [stdout] 239 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:239:71
[INFO] [stdout]     |
[INFO] [stdout] 239 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:240:38
[INFO] [stdout]     |
[INFO] [stdout] 240 |             dp_matrix.get_special(0, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:242:47
[INFO] [stdout]     |
[INFO] [stdout] 242 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/backward.rs:242:71
[INFO] [stdout]     |
[INFO] [stdout] 242 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]     |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated macro `util::log_sum`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/forward.rs:1:12
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::log_sum;
[INFO] [stdout]   |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/forward.rs:2:32
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::structs::dp_matrix::DpMatrix;
[INFO] [stdout]   |                                ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/forward.rs:3:22
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/forward.rs:3:31
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/forward.rs:4:18
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::util::log_add;
[INFO] [stdout]   |                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/forward.rs:6:26
[INFO] [stdout]   |
[INFO] [stdout] 6 | pub fn forward(profile: &Profile, target: &Sequence, dp_matrix: &mut impl DpMatrix) -> f32 {
[INFO] [stdout]   |                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/forward.rs:6:44
[INFO] [stdout]   |
[INFO] [stdout] 6 | pub fn forward(profile: &Profile, target: &Sequence, dp_matrix: &mut impl DpMatrix) -> f32 {
[INFO] [stdout]   |                                            ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/forward.rs:6:75
[INFO] [stdout]   |
[INFO] [stdout] 6 | pub fn forward(profile: &Profile, target: &Sequence, dp_matrix: &mut impl DpMatrix) -> f32 {
[INFO] [stdout]   |                                                                           ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:10:30
[INFO] [stdout]    |
[INFO] [stdout] 10 |     dp_matrix.set_special(0, Profile::SPECIAL_N_IDX, 0.0);
[INFO] [stdout]    |                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:13:9
[INFO] [stdout]    |
[INFO] [stdout] 13 |         Profile::SPECIAL_B_IDX,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:14:42
[INFO] [stdout]    |
[INFO] [stdout] 14 |         profile.special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:14:66
[INFO] [stdout]    |
[INFO] [stdout] 14 |         profile.special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:16:30
[INFO] [stdout]    |
[INFO] [stdout] 16 |     dp_matrix.set_special(0, Profile::SPECIAL_E_IDX, -f32::INFINITY);
[INFO] [stdout]    |                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:17:30
[INFO] [stdout]    |
[INFO] [stdout] 17 |     dp_matrix.set_special(0, Profile::SPECIAL_C_IDX, -f32::INFINITY);
[INFO] [stdout]    |                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:18:30
[INFO] [stdout]    |
[INFO] [stdout] 18 |     dp_matrix.set_special(0, Profile::SPECIAL_J_IDX, -f32::INFINITY);
[INFO] [stdout]    |                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:33:43
[INFO] [stdout]    |
[INFO] [stdout] 33 |         dp_matrix.set_special(target_idx, Profile::SPECIAL_E_IDX, -f32::INFINITY);
[INFO] [stdout]    |                                           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:40:17
[INFO] [stdout]     |
[INFO] [stdout]  40 | /                 log_sum!(
[INFO] [stdout]  41 | |                     dp_matrix.get_match(target_idx - 1, profile_idx - 1)
[INFO] [stdout]  42 | |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]  43 | |                     dp_matrix.get_insert(target_idx - 1, profile_idx - 1)
[INFO] [stdout] ...   |
[INFO] [stdout]  48 | |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]  49 | |                 ) + profile.match_score(current_target_character as usize, profile_idx),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:42:52
[INFO] [stdout]    |
[INFO] [stdout] 42 |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:40:17
[INFO] [stdout]     |
[INFO] [stdout]  40 | /                 log_sum!(
[INFO] [stdout]  41 | |                     dp_matrix.get_match(target_idx - 1, profile_idx - 1)
[INFO] [stdout]  42 | |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]  43 | |                     dp_matrix.get_insert(target_idx - 1, profile_idx - 1)
[INFO] [stdout] ...   |
[INFO] [stdout]  48 | |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]  49 | |                 ) + profile.match_score(current_target_character as usize, profile_idx),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:44:52
[INFO] [stdout]    |
[INFO] [stdout] 44 |                         + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:40:17
[INFO] [stdout]     |
[INFO] [stdout]  40 | /                 log_sum!(
[INFO] [stdout]  41 | |                     dp_matrix.get_match(target_idx - 1, profile_idx - 1)
[INFO] [stdout]  42 | |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]  43 | |                     dp_matrix.get_insert(target_idx - 1, profile_idx - 1)
[INFO] [stdout] ...   |
[INFO] [stdout]  48 | |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]  49 | |                 ) + profile.match_score(current_target_character as usize, profile_idx),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:45:59
[INFO] [stdout]    |
[INFO] [stdout] 45 |                     dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]    |                                                           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:46:52
[INFO] [stdout]    |
[INFO] [stdout] 46 |                         + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:48:52
[INFO] [stdout]    |
[INFO] [stdout] 48 |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:56:17
[INFO] [stdout]     |
[INFO] [stdout]  56 | /                 log_sum!(
[INFO] [stdout]  57 | |                     dp_matrix.get_match(target_idx - 1, profile_idx)
[INFO] [stdout]  58 | |                         + profile.transition_score(Profile::MATCH_TO_INSERT_IDX, profile_idx),
[INFO] [stdout]  59 | |                     dp_matrix.get_insert(target_idx - 1, profile_idx)
[INFO] [stdout]  60 | |                         + profile.transition_score(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]  61 | |                 ) + profile.insert_score(current_target_character as usize, profile_idx),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:58:52
[INFO] [stdout]    |
[INFO] [stdout] 58 |                         + profile.transition_score(Profile::MATCH_TO_INSERT_IDX, profile_idx),
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:60:52
[INFO] [stdout]    |
[INFO] [stdout] 60 |                         + profile.transition_score(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:68:17
[INFO] [stdout]     |
[INFO] [stdout]  68 | /                 log_sum!(
[INFO] [stdout]  69 | |                     dp_matrix.get_match(target_idx, profile_idx - 1)
[INFO] [stdout]  70 | |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx - 1),
[INFO] [stdout]  71 | |                     dp_matrix.get_delete(target_idx, profile_idx - 1)
[INFO] [stdout]  72 | |                         + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]  73 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:70:52
[INFO] [stdout]    |
[INFO] [stdout] 70 |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx - 1),
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:72:52
[INFO] [stdout]    |
[INFO] [stdout] 72 |                         + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:79:17
[INFO] [stdout]    |
[INFO] [stdout] 79 |                 Profile::SPECIAL_E_IDX,
[INFO] [stdout]    |                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:80:17
[INFO] [stdout]     |
[INFO] [stdout]  80 | /                 log_sum!(
[INFO] [stdout]  81 | |                     dp_matrix.get_match(target_idx, profile_idx) + end_score,
[INFO] [stdout]  82 | |                     dp_matrix.get_delete(target_idx, profile_idx) + end_score,
[INFO] [stdout]  83 | |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]  84 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:80:17
[INFO] [stdout]     |
[INFO] [stdout]  80 | /                 log_sum!(
[INFO] [stdout]  81 | |                     dp_matrix.get_match(target_idx, profile_idx) + end_score,
[INFO] [stdout]  82 | |                     dp_matrix.get_delete(target_idx, profile_idx) + end_score,
[INFO] [stdout]  83 | |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]  84 | |                 ),
[INFO] [stdout]     | |_________________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:83:55
[INFO] [stdout]    |
[INFO] [stdout] 83 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]    |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:92:13
[INFO] [stdout]     |
[INFO] [stdout]  92 | /             log_sum!(
[INFO] [stdout]  93 | |                 dp_matrix.get_match(target_idx - 1, profile.length - 1)
[INFO] [stdout]  94 | |                     + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile.length - 1),
[INFO] [stdout]  95 | |                 dp_matrix.get_insert(target_idx - 1, profile.length - 1)
[INFO] [stdout] ...   |
[INFO] [stdout] 100 | |                     + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile.length - 1)
[INFO] [stdout] 101 | |             ) + profile.match_score(current_target_character as usize, profile.length),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:94:48
[INFO] [stdout]    |
[INFO] [stdout] 94 |                     + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile.length - 1),
[INFO] [stdout]    |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:92:13
[INFO] [stdout]     |
[INFO] [stdout]  92 | /             log_sum!(
[INFO] [stdout]  93 | |                 dp_matrix.get_match(target_idx - 1, profile.length - 1)
[INFO] [stdout]  94 | |                     + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile.length - 1),
[INFO] [stdout]  95 | |                 dp_matrix.get_insert(target_idx - 1, profile.length - 1)
[INFO] [stdout] ...   |
[INFO] [stdout] 100 | |                     + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile.length - 1)
[INFO] [stdout] 101 | |             ) + profile.match_score(current_target_character as usize, profile.length),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:96:48
[INFO] [stdout]    |
[INFO] [stdout] 96 |                     + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, profile.length - 1),
[INFO] [stdout]    |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:92:13
[INFO] [stdout]     |
[INFO] [stdout]  92 | /             log_sum!(
[INFO] [stdout]  93 | |                 dp_matrix.get_match(target_idx - 1, profile.length - 1)
[INFO] [stdout]  94 | |                     + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile.length - 1),
[INFO] [stdout]  95 | |                 dp_matrix.get_insert(target_idx - 1, profile.length - 1)
[INFO] [stdout] ...   |
[INFO] [stdout] 100 | |                     + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile.length - 1)
[INFO] [stdout] 101 | |             ) + profile.match_score(current_target_character as usize, profile.length),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:97:55
[INFO] [stdout]    |
[INFO] [stdout] 97 |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]    |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/forward.rs:98:48
[INFO] [stdout]    |
[INFO] [stdout] 98 |                     + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile.length - 1),
[INFO] [stdout]    |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:100:48
[INFO] [stdout]     |
[INFO] [stdout] 100 |                     + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile.length - 1)
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:111:13
[INFO] [stdout]     |
[INFO] [stdout] 111 | /             log_sum!(
[INFO] [stdout] 112 | |                 dp_matrix.get_match(target_idx, profile.length - 1)
[INFO] [stdout] 113 | |                     + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile.length - 1),
[INFO] [stdout] 114 | |                 dp_matrix.get_delete(target_idx, profile.length - 1)
[INFO] [stdout] 115 | |                     + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile.length - 1)
[INFO] [stdout] 116 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:113:48
[INFO] [stdout]     |
[INFO] [stdout] 113 |                     + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile.length - 1),
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:115:48
[INFO] [stdout]     |
[INFO] [stdout] 115 |                     + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile.length - 1)
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:122:13
[INFO] [stdout]     |
[INFO] [stdout] 122 |             Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:123:13
[INFO] [stdout]     |
[INFO] [stdout] 123 | /             log_sum!(
[INFO] [stdout] 124 | |                 dp_matrix.get_match(target_idx, profile.length),
[INFO] [stdout] 125 | |                 dp_matrix.get_delete(target_idx, profile.length),
[INFO] [stdout] 126 | |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout] 127 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:123:13
[INFO] [stdout]     |
[INFO] [stdout] 123 | /             log_sum!(
[INFO] [stdout] 124 | |                 dp_matrix.get_match(target_idx, profile.length),
[INFO] [stdout] 125 | |                 dp_matrix.get_delete(target_idx, profile.length),
[INFO] [stdout] 126 | |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout] 127 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:126:51
[INFO] [stdout]     |
[INFO] [stdout] 126 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:133:13
[INFO] [stdout]     |
[INFO] [stdout] 133 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:134:13
[INFO] [stdout]     |
[INFO] [stdout] 134 | /             log_sum!(
[INFO] [stdout] 135 | |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout] 136 | |                     + profile.special_transition_score(
[INFO] [stdout] 137 | |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout] ...   |
[INFO] [stdout] 145 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:135:55
[INFO] [stdout]     |
[INFO] [stdout] 135 |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:137:25
[INFO] [stdout]     |
[INFO] [stdout] 137 |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:138:25
[INFO] [stdout]     |
[INFO] [stdout] 138 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:140:51
[INFO] [stdout]     |
[INFO] [stdout] 140 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:142:25
[INFO] [stdout]     |
[INFO] [stdout] 142 |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:143:25
[INFO] [stdout]     |
[INFO] [stdout] 143 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:151:13
[INFO] [stdout]     |
[INFO] [stdout] 151 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:152:13
[INFO] [stdout]     |
[INFO] [stdout] 152 | /             log_sum!(
[INFO] [stdout] 153 | |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout] 154 | |                     + profile.special_transition_score(
[INFO] [stdout] 155 | |                         Profile::SPECIAL_C_IDX,
[INFO] [stdout] ...   |
[INFO] [stdout] 163 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:153:55
[INFO] [stdout]     |
[INFO] [stdout] 153 |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:155:25
[INFO] [stdout]     |
[INFO] [stdout] 155 |                         Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:156:25
[INFO] [stdout]     |
[INFO] [stdout] 156 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:158:51
[INFO] [stdout]     |
[INFO] [stdout] 158 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:160:25
[INFO] [stdout]     |
[INFO] [stdout] 160 |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:161:25
[INFO] [stdout]     |
[INFO] [stdout] 161 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:169:13
[INFO] [stdout]     |
[INFO] [stdout] 169 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:170:51
[INFO] [stdout]     |
[INFO] [stdout] 170 |             dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:172:47
[INFO] [stdout]     |
[INFO] [stdout] 172 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:172:71
[INFO] [stdout]     |
[INFO] [stdout] 172 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:178:13
[INFO] [stdout]     |
[INFO] [stdout] 178 |             Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/forward.rs:179:13
[INFO] [stdout]     |
[INFO] [stdout] 179 | /             log_sum!(
[INFO] [stdout] 180 | |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX)
[INFO] [stdout] 181 | |                     + profile.special_transition_score(
[INFO] [stdout] 182 | |                         Profile::SPECIAL_N_IDX,
[INFO] [stdout] ...   |
[INFO] [stdout] 190 | |             ),
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:180:51
[INFO] [stdout]     |
[INFO] [stdout] 180 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:182:25
[INFO] [stdout]     |
[INFO] [stdout] 182 |                         Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:183:25
[INFO] [stdout]     |
[INFO] [stdout] 183 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:185:51
[INFO] [stdout]     |
[INFO] [stdout] 185 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:187:25
[INFO] [stdout]     |
[INFO] [stdout] 187 |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:188:25
[INFO] [stdout]     |
[INFO] [stdout] 188 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/forward.rs:194:42
[INFO] [stdout]     |
[INFO] [stdout] 194 |     dp_matrix.get_special(target.length, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                          ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated macro `util::log_sum`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/null2.rs:1:12
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::log_sum;
[INFO] [stdout]   |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/null2.rs:2:32
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::structs::dp_matrix::DpMatrix;
[INFO] [stdout]   |                                ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/null2.rs:3:22
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/null2.rs:3:31
[INFO] [stdout]   |
[INFO] [stdout] 3 | use crate::structs::{Profile, Sequence};
[INFO] [stdout]   |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/null2.rs:4:19
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::util::{log_add, LogAbuse};
[INFO] [stdout]   |                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `util::LogAbuse`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/null2.rs:4:28
[INFO] [stdout]   |
[INFO] [stdout] 4 | use crate::util::{log_add, LogAbuse};
[INFO] [stdout]   |                            ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/null2.rs:6:64
[INFO] [stdout]   |
[INFO] [stdout] 6 | pub fn null2_score(posterior_matrix: &impl DpMatrix, profile: &Profile, target: &Sequence) -> f32 {
[INFO] [stdout]   |                                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/null2.rs:6:82
[INFO] [stdout]   |
[INFO] [stdout] 6 | pub fn null2_score(posterior_matrix: &impl DpMatrix, profile: &Profile, target: &Sequence) -> f32 {
[INFO] [stdout]   |                                                                                  ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/null2.rs:6:44
[INFO] [stdout]   |
[INFO] [stdout] 6 | pub fn null2_score(posterior_matrix: &impl DpMatrix, profile: &Profile, target: &Sequence) -> f32 {
[INFO] [stdout]   |                                            ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/null2.rs:24:61
[INFO] [stdout]    |
[INFO] [stdout] 24 |         n_value += posterior_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX);
[INFO] [stdout]    |                                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/null2.rs:25:61
[INFO] [stdout]    |
[INFO] [stdout] 25 |         j_value += posterior_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX);
[INFO] [stdout]    |                                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/null2.rs:26:61
[INFO] [stdout]    |
[INFO] [stdout] 26 |         c_value += posterior_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX);
[INFO] [stdout]    |                                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/null2.rs:48:52
[INFO] [stdout]    |
[INFO] [stdout] 48 |     let mut null2: Vec<f32> = vec![-f32::INFINITY; Profile::MAX_DEGENERATE_ALPHABET_SIZE];
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |         log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/null2.rs:49:20
[INFO] [stdout]     |
[INFO] [stdout]  49 |     let x_factor = log_sum!(n_value, j_value, c_value);
[INFO] [stdout]     |                    ----------------------------------- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |         log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/null2.rs:49:20
[INFO] [stdout]     |
[INFO] [stdout]  49 |     let x_factor = log_sum!(n_value, j_value, c_value);
[INFO] [stdout]     |                    ----------------------------------- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/null2.rs:51:28
[INFO] [stdout]    |
[INFO] [stdout] 51 |     for alphabet_idx in 0..Profile::MAX_ALPHABET_SIZE {
[INFO] [stdout]    |                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/null2.rs:53:35
[INFO] [stdout]     |
[INFO] [stdout]  53 |               null2[alphabet_idx] = log_sum!(
[INFO] [stdout]     |  ___________________________________-
[INFO] [stdout]  54 | |                 null2[alphabet_idx],
[INFO] [stdout]  55 | |                 match_values[profile_idx] + profile.match_score(alphabet_idx, profile_idx),
[INFO] [stdout]  56 | |                 insert_values[profile_idx] + profile.insert_score(alphabet_idx, profile_idx)
[INFO] [stdout]  57 | |             );
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/null2.rs:53:35
[INFO] [stdout]     |
[INFO] [stdout]  53 |               null2[alphabet_idx] = log_sum!(
[INFO] [stdout]     |  ___________________________________-
[INFO] [stdout]  54 | |                 null2[alphabet_idx],
[INFO] [stdout]  55 | |                 match_values[profile_idx] + profile.match_score(alphabet_idx, profile_idx),
[INFO] [stdout]  56 | |                 insert_values[profile_idx] + profile.insert_score(alphabet_idx, profile_idx)
[INFO] [stdout]  57 | |             );
[INFO] [stdout]     | |_____________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/null2.rs:59:31
[INFO] [stdout]     |
[INFO] [stdout]  59 |           null2[alphabet_idx] = log_sum!(
[INFO] [stdout]     |  _______________________________-
[INFO] [stdout]  60 | |             null2[alphabet_idx],
[INFO] [stdout]  61 | |             match_values[profile.length] + profile.match_score(alphabet_idx, profile.length),
[INFO] [stdout]  62 | |             x_factor
[INFO] [stdout]  63 | |         );
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |           log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/null2.rs:59:31
[INFO] [stdout]     |
[INFO] [stdout]  59 |           null2[alphabet_idx] = log_sum!(
[INFO] [stdout]     |  _______________________________-
[INFO] [stdout]  60 | |             null2[alphabet_idx],
[INFO] [stdout]  61 | |             match_values[profile.length] + profile.match_score(alphabet_idx, profile.length),
[INFO] [stdout]  62 | |             x_factor
[INFO] [stdout]  63 | |         );
[INFO] [stdout]     | |_________- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/null2.rs:98:11
[INFO] [stdout]    |
[INFO] [stdout] 98 |     null2[Profile::GAP_INDEX] = 1.0;
[INFO] [stdout]    |           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/null2.rs:99:11
[INFO] [stdout]    |
[INFO] [stdout] 99 |     null2[Profile::NON_RESIDUE_IDX] = 1.0;
[INFO] [stdout]    |           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/null2.rs:100:11
[INFO] [stdout]     |
[INFO] [stdout] 100 |     null2[Profile::MISSING_DATA_IDX] = 1.0;
[INFO] [stdout]     |           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::log_add`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/util.rs:132:9
[INFO] [stdout]     |
[INFO] [stdout] 132 |         log_add($x, log_sum!($($y),+))
[INFO] [stdout]     |         ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]    ::: src/align/naive/null2.rs:111:19
[INFO] [stdout]     |
[INFO] [stdout] 111 |     null2_score = log_sum!(0.0, null2_prior + null2_score);
[INFO] [stdout]     |                   ---------------------------------------- in this macro invocation
[INFO] [stdout]     |
[INFO] [stdout]     = note: this warning originates in the macro `log_sum` (in Nightly builds, run with -Z macro-backtrace for more info)
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/optimal_accuracy.rs:1:32
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::structs::dp_matrix::DpMatrix;
[INFO] [stdout]   |                                ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/optimal_accuracy.rs:2:21
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::structs::Profile;
[INFO] [stdout]   |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/optimal_accuracy.rs:5:15
[INFO] [stdout]   |
[INFO] [stdout] 5 |     profile: &Profile,
[INFO] [stdout]   |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/optimal_accuracy.rs:6:29
[INFO] [stdout]   |
[INFO] [stdout] 6 |     posterior_matrix: &impl DpMatrix,
[INFO] [stdout]   |                             ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/optimal_accuracy.rs:7:31
[INFO] [stdout]   |
[INFO] [stdout] 7 |     optimal_matrix: &mut impl DpMatrix,
[INFO] [stdout]   |                               ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:12:35
[INFO] [stdout]    |
[INFO] [stdout] 12 |     optimal_matrix.set_special(0, Profile::SPECIAL_N_IDX, 0.0);
[INFO] [stdout]    |                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:13:35
[INFO] [stdout]    |
[INFO] [stdout] 13 |     optimal_matrix.set_special(0, Profile::SPECIAL_B_IDX, 0.0);
[INFO] [stdout]    |                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:14:35
[INFO] [stdout]    |
[INFO] [stdout] 14 |     optimal_matrix.set_special(0, Profile::SPECIAL_E_IDX, -f32::INFINITY);
[INFO] [stdout]    |                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:15:35
[INFO] [stdout]    |
[INFO] [stdout] 15 |     optimal_matrix.set_special(0, Profile::SPECIAL_C_IDX, -f32::INFINITY);
[INFO] [stdout]    |                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:16:35
[INFO] [stdout]    |
[INFO] [stdout] 16 |     optimal_matrix.set_special(0, Profile::SPECIAL_J_IDX, -f32::INFINITY);
[INFO] [stdout]    |                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:28:39
[INFO] [stdout]    |
[INFO] [stdout] 28 |         optimal_matrix.set_special(i, Profile::SPECIAL_E_IDX, -f32::INFINITY);
[INFO] [stdout]    |                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:36:56
[INFO] [stdout]    |
[INFO] [stdout] 36 |                         profile.transition_score_delta(Profile::MATCH_TO_MATCH_IDX, k - 1)
[INFO] [stdout]    |                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:39:56
[INFO] [stdout]    |
[INFO] [stdout] 39 |                         profile.transition_score_delta(Profile::INSERT_TO_MATCH_IDX, k - 1)
[INFO] [stdout]    |                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:44:56
[INFO] [stdout]    |
[INFO] [stdout] 44 |                         profile.transition_score_delta(Profile::DELETE_TO_MATCH_IDX, k - 1)
[INFO] [stdout]    |                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:47:56
[INFO] [stdout]    |
[INFO] [stdout] 47 |                         profile.transition_score_delta(Profile::BEGIN_TO_MATCH_IDX, k - 1)
[INFO] [stdout]    |                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:48:66
[INFO] [stdout]    |
[INFO] [stdout] 48 | ...                   * (optimal_matrix.get_special(i - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]    |                                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:59:17
[INFO] [stdout]    |
[INFO] [stdout] 59 |                 Profile::SPECIAL_E_IDX,
[INFO] [stdout]    |                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:61:51
[INFO] [stdout]    |
[INFO] [stdout] 61 |                     optimal_matrix.get_special(i, Profile::SPECIAL_E_IDX),
[INFO] [stdout]    |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:70:52
[INFO] [stdout]    |
[INFO] [stdout] 70 |                     profile.transition_score_delta(Profile::MATCH_TO_INSERT_IDX, k)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:72:52
[INFO] [stdout]    |
[INFO] [stdout] 72 |                     profile.transition_score_delta(Profile::INSERT_TO_INSERT_IDX, k)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:81:52
[INFO] [stdout]    |
[INFO] [stdout] 81 |                     profile.transition_score_delta(Profile::MATCH_TO_DELETE_IDX, k - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:83:52
[INFO] [stdout]    |
[INFO] [stdout] 83 |                     profile.transition_score_delta(Profile::DELETE_TO_DELETE_IDX, k - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:94:52
[INFO] [stdout]    |
[INFO] [stdout] 94 |                     profile.transition_score_delta(Profile::MATCH_TO_MATCH_IDX, profile.length - 1)
[INFO] [stdout]    |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/optimal_accuracy.rs:98:49
[INFO] [stdout]    |
[INFO] [stdout] 98 |                         .transition_score_delta(Profile::INSERT_TO_MATCH_IDX, profile.length - 1)
[INFO] [stdout]    |                                                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:104:49
[INFO] [stdout]     |
[INFO] [stdout] 104 |                         .transition_score_delta(Profile::DELETE_TO_MATCH_IDX, profile.length - 1)
[INFO] [stdout]     |                                                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:107:52
[INFO] [stdout]     |
[INFO] [stdout] 107 |                     profile.transition_score_delta(Profile::BEGIN_TO_MATCH_IDX, profile.length - 1)
[INFO] [stdout]     |                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:108:62
[INFO] [stdout]     |
[INFO] [stdout] 108 |                         * (optimal_matrix.get_special(i - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                                              ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:118:48
[INFO] [stdout]     |
[INFO] [stdout] 118 |                 profile.transition_score_delta(Profile::MATCH_TO_DELETE_IDX, profile.length - 1)
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:120:48
[INFO] [stdout]     |
[INFO] [stdout] 120 |                 profile.transition_score_delta(Profile::DELETE_TO_DELETE_IDX, profile.length - 1)
[INFO] [stdout]     |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:129:13
[INFO] [stdout]     |
[INFO] [stdout] 129 |             Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:131:47
[INFO] [stdout]     |
[INFO] [stdout] 131 |                 optimal_matrix.get_special(i, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:141:13
[INFO] [stdout]     |
[INFO] [stdout] 141 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:144:21
[INFO] [stdout]     |
[INFO] [stdout] 144 |                     Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:145:21
[INFO] [stdout]     |
[INFO] [stdout] 145 |                     Profile::SPECIAL_LOOP_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:146:56
[INFO] [stdout]     |
[INFO] [stdout] 146 |                 ) * (optimal_matrix.get_special(i - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:147:55
[INFO] [stdout]     |
[INFO] [stdout] 147 |                     + posterior_matrix.get_special(i, Profile::SPECIAL_J_IDX)),
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:149:21
[INFO] [stdout]     |
[INFO] [stdout] 149 |                     Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:150:21
[INFO] [stdout]     |
[INFO] [stdout] 150 |                     Profile::SPECIAL_LOOP_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:151:51
[INFO] [stdout]     |
[INFO] [stdout] 151 |                 ) * optimal_matrix.get_special(i, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:157:13
[INFO] [stdout]     |
[INFO] [stdout] 157 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:160:21
[INFO] [stdout]     |
[INFO] [stdout] 160 |                     Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:161:21
[INFO] [stdout]     |
[INFO] [stdout] 161 |                     Profile::SPECIAL_LOOP_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:162:56
[INFO] [stdout]     |
[INFO] [stdout] 162 |                 ) * (optimal_matrix.get_special(i - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:163:55
[INFO] [stdout]     |
[INFO] [stdout] 163 |                     + posterior_matrix.get_special(i, Profile::SPECIAL_C_IDX)),
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:165:21
[INFO] [stdout]     |
[INFO] [stdout] 165 |                     Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:166:21
[INFO] [stdout]     |
[INFO] [stdout] 166 |                     Profile::SPECIAL_MOVE_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:167:51
[INFO] [stdout]     |
[INFO] [stdout] 167 |                 ) * optimal_matrix.get_special(i, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:173:13
[INFO] [stdout]     |
[INFO] [stdout] 173 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:175:49
[INFO] [stdout]     |
[INFO] [stdout] 175 |                 .special_transition_score_delta(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                                                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:175:73
[INFO] [stdout]     |
[INFO] [stdout] 175 |                 .special_transition_score_delta(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                                                                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:176:54
[INFO] [stdout]     |
[INFO] [stdout] 176 |                 * (optimal_matrix.get_special(i - 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                      ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:177:55
[INFO] [stdout]     |
[INFO] [stdout] 177 |                     + posterior_matrix.get_special(i, Profile::SPECIAL_N_IDX)),
[INFO] [stdout]     |                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:182:13
[INFO] [stdout]     |
[INFO] [stdout] 182 |             Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:185:21
[INFO] [stdout]     |
[INFO] [stdout] 185 |                     Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:186:21
[INFO] [stdout]     |
[INFO] [stdout] 186 |                     Profile::SPECIAL_MOVE_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:187:51
[INFO] [stdout]     |
[INFO] [stdout] 187 |                 ) * optimal_matrix.get_special(i, Profile::SPECIAL_N_IDX),
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:189:21
[INFO] [stdout]     |
[INFO] [stdout] 189 |                     Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:190:21
[INFO] [stdout]     |
[INFO] [stdout] 190 |                     Profile::SPECIAL_MOVE_IDX,
[INFO] [stdout]     |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/optimal_accuracy.rs:191:51
[INFO] [stdout]     |
[INFO] [stdout] 191 |                 ) * optimal_matrix.get_special(i, Profile::SPECIAL_J_IDX),
[INFO] [stdout]     |                                                   ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/posterior.rs:1:32
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::structs::dp_matrix::DpMatrix;
[INFO] [stdout]   |                                ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/posterior.rs:2:21
[INFO] [stdout]   |
[INFO] [stdout] 2 | use crate::structs::Profile;
[INFO] [stdout]   |                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/posterior.rs:5:15
[INFO] [stdout]   |
[INFO] [stdout] 5 |     profile: &Profile,
[INFO] [stdout]   |               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/posterior.rs:6:27
[INFO] [stdout]   |
[INFO] [stdout] 6 |     forward_matrix: &impl DpMatrix,
[INFO] [stdout]   |                           ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/posterior.rs:7:28
[INFO] [stdout]   |
[INFO] [stdout] 7 |     backward_matrix: &impl DpMatrix,
[INFO] [stdout]   |                            ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `structs::dp_matrix::DpMatrix`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/naive/posterior.rs:8:33
[INFO] [stdout]   |
[INFO] [stdout] 8 |     posterior_matrix: &mut impl DpMatrix,
[INFO] [stdout]   |                                 ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:11:72
[INFO] [stdout]    |
[INFO] [stdout] 11 |     let overall_score: f32 = forward_matrix.get_special(target_length, Profile::SPECIAL_C_IDX)
[INFO] [stdout]    |                                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:12:44
[INFO] [stdout]    |
[INFO] [stdout] 12 |         + profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX);
[INFO] [stdout]    |                                            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:12:68
[INFO] [stdout]    |
[INFO] [stdout] 12 |         + profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX);
[INFO] [stdout]    |                                                                    ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:15:37
[INFO] [stdout]    |
[INFO] [stdout] 15 |     posterior_matrix.set_special(0, Profile::SPECIAL_E_IDX, 0.0);
[INFO] [stdout]    |                                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:16:37
[INFO] [stdout]    |
[INFO] [stdout] 16 |     posterior_matrix.set_special(0, Profile::SPECIAL_N_IDX, 0.0);
[INFO] [stdout]    |                                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:17:37
[INFO] [stdout]    |
[INFO] [stdout] 17 |     posterior_matrix.set_special(0, Profile::SPECIAL_J_IDX, 0.0);
[INFO] [stdout]    |                                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:18:37
[INFO] [stdout]    |
[INFO] [stdout] 18 |     posterior_matrix.set_special(0, Profile::SPECIAL_B_IDX, 0.0);
[INFO] [stdout]    |                                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:19:37
[INFO] [stdout]    |
[INFO] [stdout] 19 |     posterior_matrix.set_special(0, Profile::SPECIAL_C_IDX, 0.0);
[INFO] [stdout]    |                                     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:68:41
[INFO] [stdout]    |
[INFO] [stdout] 68 |         posterior_matrix.set_special(i, Profile::SPECIAL_E_IDX, 0.0);
[INFO] [stdout]    |                                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:71:13
[INFO] [stdout]    |
[INFO] [stdout] 71 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]    |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:72:48
[INFO] [stdout]    |
[INFO] [stdout] 72 |             (forward_matrix.get_special(i - 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]    |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:73:50
[INFO] [stdout]    |
[INFO] [stdout] 73 |                 + backward_matrix.get_special(i, Profile::SPECIAL_N_IDX)
[INFO] [stdout]    |                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:75:47
[INFO] [stdout]    |
[INFO] [stdout] 75 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]    |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:75:71
[INFO] [stdout]    |
[INFO] [stdout] 75 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]    |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:82:13
[INFO] [stdout]    |
[INFO] [stdout] 82 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]    |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:83:48
[INFO] [stdout]    |
[INFO] [stdout] 83 |             (forward_matrix.get_special(i - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]    |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:84:50
[INFO] [stdout]    |
[INFO] [stdout] 84 |                 + backward_matrix.get_special(i, Profile::SPECIAL_J_IDX)
[INFO] [stdout]    |                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:86:47
[INFO] [stdout]    |
[INFO] [stdout] 86 |                     .special_transition_score(Profile::SPECIAL_J_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]    |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:86:71
[INFO] [stdout]    |
[INFO] [stdout] 86 |                     .special_transition_score(Profile::SPECIAL_J_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]    |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:91:41
[INFO] [stdout]    |
[INFO] [stdout] 91 |         posterior_matrix.set_special(i, Profile::SPECIAL_B_IDX, 0.0);
[INFO] [stdout]    |                                         ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:95:13
[INFO] [stdout]    |
[INFO] [stdout] 95 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]    |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:96:48
[INFO] [stdout]    |
[INFO] [stdout] 96 |             (forward_matrix.get_special(i - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]    |                                                ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:97:50
[INFO] [stdout]    |
[INFO] [stdout] 97 |                 + backward_matrix.get_special(i, Profile::SPECIAL_C_IDX)
[INFO] [stdout]    |                                                  ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:99:47
[INFO] [stdout]    |
[INFO] [stdout] 99 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]    |                                               ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/naive/posterior.rs:99:71
[INFO] [stdout]    |
[INFO] [stdout] 99 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]    |                                                                       ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/posterior.rs:104:56
[INFO] [stdout]     |
[INFO] [stdout] 104 |         denominator += posterior_matrix.get_special(i, Profile::SPECIAL_N_IDX);
[INFO] [stdout]     |                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/posterior.rs:105:56
[INFO] [stdout]     |
[INFO] [stdout] 105 |         denominator += posterior_matrix.get_special(i, Profile::SPECIAL_J_IDX);
[INFO] [stdout]     |                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/posterior.rs:106:56
[INFO] [stdout]     |
[INFO] [stdout] 106 |         denominator += posterior_matrix.get_special(i, Profile::SPECIAL_C_IDX);
[INFO] [stdout]     |                                                        ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/posterior.rs:121:13
[INFO] [stdout]     |
[INFO] [stdout] 121 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/posterior.rs:122:45
[INFO] [stdout]     |
[INFO] [stdout] 122 |             posterior_matrix.get_special(i, Profile::SPECIAL_N_IDX) * denominator,
[INFO] [stdout]     |                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/posterior.rs:126:13
[INFO] [stdout]     |
[INFO] [stdout] 126 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/posterior.rs:127:45
[INFO] [stdout]     |
[INFO] [stdout] 127 |             posterior_matrix.get_special(i, Profile::SPECIAL_J_IDX) * denominator,
[INFO] [stdout]     |                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/posterior.rs:131:13
[INFO] [stdout]     |
[INFO] [stdout] 131 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::profile::Profile`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/naive/posterior.rs:132:45
[INFO] [stdout]     |
[INFO] [stdout] 132 |             posterior_matrix.get_special(i, Profile::SPECIAL_C_IDX) * denominator,
[INFO] [stdout]     |                                             ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/align/needleman_wunsch.rs:1:21
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::structs::Sequence;
[INFO] [stdout]   |                     ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/needleman_wunsch.rs:22:53
[INFO] [stdout]    |
[INFO] [stdout] 22 | pub fn print_alignment(trace: &SimpleTrace, seq_1: &Sequence, seq_2: &Sequence) {
[INFO] [stdout]    |                                                     ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/needleman_wunsch.rs:22:71
[INFO] [stdout]    |
[INFO] [stdout] 22 | pub fn print_alignment(trace: &SimpleTrace, seq_1: &Sequence, seq_2: &Sequence) {
[INFO] [stdout]    |                                                                       ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/needleman_wunsch.rs:63:33
[INFO] [stdout]    |
[INFO] [stdout] 63 | pub fn needleman_wunsch(seq_1: &Sequence, seq_2: &Sequence) -> SimpleTrace {
[INFO] [stdout]    |                                 ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::sequence::Sequence`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/needleman_wunsch.rs:63:51
[INFO] [stdout]    |
[INFO] [stdout] 63 | pub fn needleman_wunsch(seq_1: &Sequence, seq_2: &Sequence) -> SimpleTrace {
[INFO] [stdout]    |                                                   ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::alignment::Alignment`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/output/output_standard.rs:1:21
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::structs::Alignment;
[INFO] [stdout]   |                     ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::alignment::Alignment`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/output/output_standard.rs:5:47
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub fn write_standard_output(alignments: &Vec<Alignment>, out: &mut impl Write) -> Result<()> {
[INFO] [stdout]   |                                               ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::alignment::Alignment`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/output/output_tabular.rs:1:21
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::structs::Alignment;
[INFO] [stdout]   |                     ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `structs::alignment::Alignment`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/output/output_tabular.rs:18:46
[INFO] [stdout]    |
[INFO] [stdout] 18 | pub fn write_tabular_output(alignments: &Vec<Alignment>, out: &mut impl Write) -> Result<()> {
[INFO] [stdout]    |                                              ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_DASH`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/structs/alignment.rs:1:23
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::alphabet::{UTF8_DASH, UTF8_DOT, UTF8_NUMERIC, UTF8_PLUS, UTF8_SPACE};
[INFO] [stdout]   |                       ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_DOT`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/structs/alignment.rs:1:34
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::alphabet::{UTF8_DASH, UTF8_DOT, UTF8_NUMERIC, UTF8_PLUS, UTF8_SPACE};
[INFO] [stdout]   |                                  ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_NUMERIC`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/structs/alignment.rs:1:44
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::alphabet::{UTF8_DASH, UTF8_DOT, UTF8_NUMERIC, UTF8_PLUS, UTF8_SPACE};
[INFO] [stdout]   |                                            ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_PLUS`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/structs/alignment.rs:1:58
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::alphabet::{UTF8_DASH, UTF8_DOT, UTF8_NUMERIC, UTF8_PLUS, UTF8_SPACE};
[INFO] [stdout]   |                                                          ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_SPACE`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/structs/alignment.rs:1:69
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::alphabet::{UTF8_DASH, UTF8_DOT, UTF8_NUMERIC, UTF8_PLUS, UTF8_SPACE};
[INFO] [stdout]   |                                                                     ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_NUMERIC`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/structs/alignment.rs:55:5
[INFO] [stdout]    |
[INFO] [stdout] 55 |     UTF8_NUMERIC[bin as usize]
[INFO] [stdout]    |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_PLUS`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/structs/alignment.rs:66:9
[INFO] [stdout]    |
[INFO] [stdout] 66 |         UTF8_PLUS
[INFO] [stdout]    |         ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_SPACE`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/structs/alignment.rs:69:9
[INFO] [stdout]    |
[INFO] [stdout] 69 |         UTF8_SPACE
[INFO] [stdout]    |         ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_DOT`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/alignment.rs:146:48
[INFO] [stdout]     |
[INFO] [stdout] 146 | ...                   profile_bytes.push(UTF8_DOT);
[INFO] [stdout]     |                                          ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_SPACE`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/alignment.rs:148:44
[INFO] [stdout]     |
[INFO] [stdout] 148 | ...                   mid_bytes.push(UTF8_SPACE);
[INFO] [stdout]     |                                      ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_DASH`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/alignment.rs:152:47
[INFO] [stdout]     |
[INFO] [stdout] 152 | ...                   target_bytes.push(UTF8_DASH);
[INFO] [stdout]     |                                         ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_SPACE`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/alignment.rs:153:44
[INFO] [stdout]     |
[INFO] [stdout] 153 | ...                   mid_bytes.push(UTF8_SPACE);
[INFO] [stdout]     |                                      ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_ALPHABET_WITH_DEGENERATE`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/structs/profile.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 |     AMINO_ALPHABET_WITH_DEGENERATE, AMINO_BACKGROUND_FREQUENCIES, AMINO_INVERSE_MAP,
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_BACKGROUND_FREQUENCIES`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/structs/profile.rs:2:37
[INFO] [stdout]   |
[INFO] [stdout] 2 |     AMINO_ALPHABET_WITH_DEGENERATE, AMINO_BACKGROUND_FREQUENCIES, AMINO_INVERSE_MAP,
[INFO] [stdout]   |                                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_INVERSE_MAP`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/structs/profile.rs:2:67
[INFO] [stdout]   |
[INFO] [stdout] 2 |     AMINO_ALPHABET_WITH_DEGENERATE, AMINO_BACKGROUND_FREQUENCIES, AMINO_INVERSE_MAP,
[INFO] [stdout]   |                                                                   ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_INVERSE_MAP_LOWER`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/structs/profile.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 |     AMINO_INVERSE_MAP_LOWER, UTF8_SPACE,
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_SPACE`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/structs/profile.rs:3:30
[INFO] [stdout]   |
[INFO] [stdout] 3 |     AMINO_INVERSE_MAP_LOWER, UTF8_SPACE,
[INFO] [stdout]   |                              ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::f32_vec_argmax`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/structs/profile.rs:14:19
[INFO] [stdout]    |
[INFO] [stdout] 14 | use crate::util::{f32_vec_argmax, LogAbuse};
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated trait `util::LogAbuse`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/structs/profile.rs:14:35
[INFO] [stdout]    |
[INFO] [stdout] 14 | use crate::util::{f32_vec_argmax, LogAbuse};
[INFO] [stdout]    |                                   ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_SPACE`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/profile.rs:105:38
[INFO] [stdout]     |
[INFO] [stdout] 105 |             consensus_sequence: vec![UTF8_SPACE],
[INFO] [stdout]     |                                      ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated function `util::f32_vec_argmax`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/profile.rs:174:17
[INFO] [stdout]     |
[INFO] [stdout] 174 |                 f32_vec_argmax(&hmm.model.match_probabilities[model_position_idx]);
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_INVERSE_MAP`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/profile.rs:183:21
[INFO] [stdout]     |
[INFO] [stdout] 183 |                     AMINO_INVERSE_MAP[&(match_probabilities_argmax as u8)]
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_INVERSE_MAP_LOWER`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/profile.rs:186:21
[INFO] [stdout]     |
[INFO] [stdout] 186 |                     AMINO_INVERSE_MAP_LOWER[&(match_probabilities_argmax as u8)]
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_BACKGROUND_FREQUENCIES`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/profile.rs:194:27
[INFO] [stdout]     |
[INFO] [stdout] 194 |                         / AMINO_BACKGROUND_FREQUENCIES[alphabet_idx] as f64)
[INFO] [stdout]     |                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_BACKGROUND_FREQUENCIES`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/profile.rs:210:27
[INFO] [stdout]     |
[INFO] [stdout] 210 |                         * AMINO_BACKGROUND_FREQUENCIES[i];
[INFO] [stdout]     |                           ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_BACKGROUND_FREQUENCIES`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/profile.rs:211:36
[INFO] [stdout]     |
[INFO] [stdout] 211 |                     denominator += AMINO_BACKGROUND_FREQUENCIES[i];
[INFO] [stdout]     |                                    ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_ALPHABET_WITH_DEGENERATE`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/profile.rs:394:28
[INFO] [stdout]     |
[INFO] [stdout] 394 |             for residue in AMINO_ALPHABET_WITH_DEGENERATE {
[INFO] [stdout]     |                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_INVERSE_MAP`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/structs/sequence.rs:5:23
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::alphabet::{AMINO_INVERSE_MAP, UTF8_TO_DIGITAL_AMINO};
[INFO] [stdout]   |                       ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_TO_DIGITAL_AMINO`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/structs/sequence.rs:5:42
[INFO] [stdout]   |
[INFO] [stdout] 5 | use crate::alphabet::{AMINO_INVERSE_MAP, UTF8_TO_DIGITAL_AMINO};
[INFO] [stdout]   |                                          ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_TO_DIGITAL_AMINO`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/structs/sequence.rs:51:46
[INFO] [stdout]    |
[INFO] [stdout] 51 |                     let digital_byte = match UTF8_TO_DIGITAL_AMINO.get(utf8_byte) {
[INFO] [stdout]    |                                              ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_INVERSE_MAP`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/structs/sequence.rs:77:35
[INFO] [stdout]    |
[INFO] [stdout] 77 |             let utf8_byte = match AMINO_INVERSE_MAP.get(digital_byte) {
[INFO] [stdout]    |                                   ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::UTF8_TO_DIGITAL_AMINO`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/sequence.rs:103:38
[INFO] [stdout]     |
[INFO] [stdout] 103 |             let digital_byte = match UTF8_TO_DIGITAL_AMINO.get(utf8_byte) {
[INFO] [stdout]     |                                      ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_INVERSE_MAP`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/structs/trace.rs:20:22
[INFO] [stdout]    |
[INFO] [stdout] 20 | use crate::alphabet::AMINO_INVERSE_MAP;
[INFO] [stdout]    |                      ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated constant `alphabet::AMINO_INVERSE_MAP`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/structs/trace.rs:191:34
[INFO] [stdout]     |
[INFO] [stdout] 191 |             writeln!(out, " {}", AMINO_INVERSE_MAP[&current_residue] as char)?;
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `align::bounded::structs::bound::CloudBoundGroup`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/viz.rs:1:38
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::align::bounded::structs::{CloudBoundGroup, RowBounds};
[INFO] [stdout]   |                                      ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `align::bounded::structs::row_bounds::RowBounds`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/viz.rs:1:55
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::align::bounded::structs::{CloudBoundGroup, RowBounds};
[INFO] [stdout]   |                                                       ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `align::bounded::structs::bound::CloudBoundGroup`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]  --> src/viz.rs:6:6
[INFO] [stdout]   |
[INFO] [stdout] 6 | impl CloudBoundGroup {
[INFO] [stdout]   |      ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `align::bounded::structs::row_bounds::RowBounds`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/viz.rs:38:6
[INFO] [stdout]    |
[INFO] [stdout] 38 | impl RowBounds {
[INFO] [stdout]    |      ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::NUM_SPECIAL_STATES`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/structs/dp_matrix_sparse.rs:211:46
[INFO] [stdout]     |
[INFO] [stdout] 211 |         debug_assert!(special_idx < Profile::NUM_SPECIAL_STATES);
[INFO] [stdout]     |                                              ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::NUM_SPECIAL_STATES`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/structs/dp_matrix_sparse.rs:218:46
[INFO] [stdout]     |
[INFO] [stdout] 218 |         debug_assert!(special_idx < Profile::NUM_SPECIAL_STATES);
[INFO] [stdout]     |                                              ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::NUM_SPECIAL_STATES`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/structs/dp_matrix_sparse.rs:272:46
[INFO] [stdout]     |
[INFO] [stdout] 272 |         debug_assert!(special_idx < Profile::NUM_SPECIAL_STATES);
[INFO] [stdout]     |                                              ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::NUM_SPECIAL_STATES`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/structs/dp_matrix_sparse.rs:279:46
[INFO] [stdout]     |
[INFO] [stdout] 279 |         debug_assert!(special_idx < Profile::NUM_SPECIAL_STATES);
[INFO] [stdout]     |                                              ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:15:15
[INFO] [stdout]    |
[INFO] [stdout] 15 |     dp_matrix.set_special(bounds.target_start - 1, Profile::SPECIAL_N_IDX, 0.0);
[INFO] [stdout]    |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:15:61
[INFO] [stdout]    |
[INFO] [stdout] 15 |     dp_matrix.set_special(bounds.target_start - 1, Profile::SPECIAL_N_IDX, 0.0);
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:16:15
[INFO] [stdout]    |
[INFO] [stdout] 16 |     dp_matrix.set_special(
[INFO] [stdout]    |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:18:18
[INFO] [stdout]    |
[INFO] [stdout] 18 |         Profile::SPECIAL_B_IDX,
[INFO] [stdout]    |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:19:17
[INFO] [stdout]    |
[INFO] [stdout] 19 |         profile.special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                 ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:19:51
[INFO] [stdout]    |
[INFO] [stdout] 19 |         profile.special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                   ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_MOVE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:19:75
[INFO] [stdout]    |
[INFO] [stdout] 19 |         profile.special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                                           ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:21:15
[INFO] [stdout]    |
[INFO] [stdout] 21 |     dp_matrix.set_special(
[INFO] [stdout]    |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:23:18
[INFO] [stdout]    |
[INFO] [stdout] 23 |         Profile::SPECIAL_E_IDX,
[INFO] [stdout]    |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:26:15
[INFO] [stdout]    |
[INFO] [stdout] 26 |     dp_matrix.set_special(
[INFO] [stdout]    |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:28:18
[INFO] [stdout]    |
[INFO] [stdout] 28 |         Profile::SPECIAL_C_IDX,
[INFO] [stdout]    |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:31:15
[INFO] [stdout]    |
[INFO] [stdout] 31 |     dp_matrix.set_special(
[INFO] [stdout]    |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:33:18
[INFO] [stdout]    |
[INFO] [stdout] 33 |         Profile::SPECIAL_J_IDX,
[INFO] [stdout]    |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `structs::sequence::Sequence::digital_bytes`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:38:40
[INFO] [stdout]    |
[INFO] [stdout] 38 |         let current_target_character = target.digital_bytes[target_idx];
[INFO] [stdout]    |                                        ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:42:23
[INFO] [stdout]    |
[INFO] [stdout] 42 |             dp_matrix.set_match(
[INFO] [stdout]    |                       ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:46:31
[INFO] [stdout]    |
[INFO] [stdout] 46 |                     dp_matrix.get_match(target_idx - 1, profile_idx - 1)
[INFO] [stdout]    |                               ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:47:35
[INFO] [stdout]    |
[INFO] [stdout] 47 |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]    |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:47:61
[INFO] [stdout]    |
[INFO] [stdout] 47 |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:48:31
[INFO] [stdout]    |
[INFO] [stdout] 48 |                     dp_matrix.get_insert(target_idx - 1, profile_idx - 1)
[INFO] [stdout]    |                               ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:49:35
[INFO] [stdout]    |
[INFO] [stdout] 49 |                         + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]    |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::INSERT_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:49:61
[INFO] [stdout]    |
[INFO] [stdout] 49 |                         + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:50:31
[INFO] [stdout]    |
[INFO] [stdout] 50 |                     dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]    |                               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:50:68
[INFO] [stdout]    |
[INFO] [stdout] 50 |                     dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]    |                                                                    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:51:35
[INFO] [stdout]    |
[INFO] [stdout] 51 |                         + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]    |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::BEGIN_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:51:61
[INFO] [stdout]    |
[INFO] [stdout] 51 |                         + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1),
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:52:31
[INFO] [stdout]    |
[INFO] [stdout] 52 |                     dp_matrix.get_delete(target_idx - 1, profile_idx - 1)
[INFO] [stdout]    |                               ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:53:35
[INFO] [stdout]    |
[INFO] [stdout] 53 |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::DELETE_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:53:61
[INFO] [stdout]    |
[INFO] [stdout] 53 |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::match_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:54:29
[INFO] [stdout]    |
[INFO] [stdout] 54 |                 ) + profile.match_score(current_target_character as usize, profile_idx),
[INFO] [stdout]    |                             ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:58:23
[INFO] [stdout]    |
[INFO] [stdout] 58 |             dp_matrix.set_insert(
[INFO] [stdout]    |                       ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:62:31
[INFO] [stdout]    |
[INFO] [stdout] 62 |                     dp_matrix.get_match(target_idx - 1, profile_idx)
[INFO] [stdout]    |                               ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:63:35
[INFO] [stdout]    |
[INFO] [stdout] 63 |                         + profile.transition_score(Profile::MATCH_TO_INSERT_IDX, profile_idx),
[INFO] [stdout]    |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_INSERT_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:63:61
[INFO] [stdout]    |
[INFO] [stdout] 63 |                         + profile.transition_score(Profile::MATCH_TO_INSERT_IDX, profile_idx),
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:64:31
[INFO] [stdout]    |
[INFO] [stdout] 64 |                     dp_matrix.get_insert(target_idx - 1, profile_idx)
[INFO] [stdout]    |                               ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:65:35
[INFO] [stdout]    |
[INFO] [stdout] 65 |                         + profile.transition_score(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::INSERT_TO_INSERT_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:65:61
[INFO] [stdout]    |
[INFO] [stdout] 65 |                         + profile.transition_score(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::insert_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:66:29
[INFO] [stdout]    |
[INFO] [stdout] 66 |                 ) + profile.insert_score(current_target_character as usize, profile_idx),
[INFO] [stdout]    |                             ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:70:23
[INFO] [stdout]    |
[INFO] [stdout] 70 |             dp_matrix.set_delete(
[INFO] [stdout]    |                       ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:74:31
[INFO] [stdout]    |
[INFO] [stdout] 74 |                     dp_matrix.get_match(target_idx, profile_idx - 1)
[INFO] [stdout]    |                               ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:75:35
[INFO] [stdout]    |
[INFO] [stdout] 75 |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx - 1),
[INFO] [stdout]    |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_DELETE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:75:61
[INFO] [stdout]    |
[INFO] [stdout] 75 |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx - 1),
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:76:31
[INFO] [stdout]    |
[INFO] [stdout] 76 |                     dp_matrix.get_delete(target_idx, profile_idx - 1)
[INFO] [stdout]    |                               ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:77:35
[INFO] [stdout]    |
[INFO] [stdout] 77 |                         + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]    |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::DELETE_TO_DELETE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:77:61
[INFO] [stdout]    |
[INFO] [stdout] 77 |                         + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:82:23
[INFO] [stdout]    |
[INFO] [stdout] 82 |             dp_matrix.set_special(
[INFO] [stdout]    |                       ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:84:26
[INFO] [stdout]    |
[INFO] [stdout] 84 |                 Profile::SPECIAL_E_IDX,
[INFO] [stdout]    |                          ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:86:31
[INFO] [stdout]    |
[INFO] [stdout] 86 |                     dp_matrix.get_match(target_idx, profile_idx) + end_score,
[INFO] [stdout]    |                               ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:87:31
[INFO] [stdout]    |
[INFO] [stdout] 87 |                     dp_matrix.get_delete(target_idx, profile_idx) + end_score,
[INFO] [stdout]    |                               ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:88:31
[INFO] [stdout]    |
[INFO] [stdout] 88 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]    |                               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:88:64
[INFO] [stdout]    |
[INFO] [stdout] 88 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]    |                                                                ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/forward_bounded.rs:96:19
[INFO] [stdout]    |
[INFO] [stdout] 96 |         dp_matrix.set_match(
[INFO] [stdout]    |                   ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:100:27
[INFO] [stdout]     |
[INFO] [stdout] 100 |                 dp_matrix.get_match(target_idx - 1, last_profile_idx - 1)
[INFO] [stdout]     |                           ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:101:31
[INFO] [stdout]     |
[INFO] [stdout] 101 |                     + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, last_profile_idx - 1),
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:101:57
[INFO] [stdout]     |
[INFO] [stdout] 101 |                     + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, last_profile_idx - 1),
[INFO] [stdout]     |                                                         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:102:27
[INFO] [stdout]     |
[INFO] [stdout] 102 |                 dp_matrix.get_insert(target_idx - 1, last_profile_idx - 1)
[INFO] [stdout]     |                           ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:103:31
[INFO] [stdout]     |
[INFO] [stdout] 103 |                     + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, last_profile_idx - 1),
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::INSERT_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:103:57
[INFO] [stdout]     |
[INFO] [stdout] 103 |                     + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, last_profile_idx - 1),
[INFO] [stdout]     |                                                         ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:104:27
[INFO] [stdout]     |
[INFO] [stdout] 104 |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:104:64
[INFO] [stdout]     |
[INFO] [stdout] 104 |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                                                ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:105:31
[INFO] [stdout]     |
[INFO] [stdout] 105 |                     + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, last_profile_idx - 1),
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::BEGIN_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:105:57
[INFO] [stdout]     |
[INFO] [stdout] 105 |                     + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, last_profile_idx - 1),
[INFO] [stdout]     |                                                         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:106:27
[INFO] [stdout]     |
[INFO] [stdout] 106 |                 dp_matrix.get_delete(target_idx - 1, last_profile_idx - 1)
[INFO] [stdout]     |                           ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:107:31
[INFO] [stdout]     |
[INFO] [stdout] 107 |                     + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, last_profile_idx - 1)
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::DELETE_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:107:57
[INFO] [stdout]     |
[INFO] [stdout] 107 |                     + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, last_profile_idx - 1)
[INFO] [stdout]     |                                                         ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::match_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:108:25
[INFO] [stdout]     |
[INFO] [stdout] 108 |             ) + profile.match_score(current_target_character as usize, last_profile_idx),
[INFO] [stdout]     |                         ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:112:19
[INFO] [stdout]     |
[INFO] [stdout] 112 |         dp_matrix.set_insert(target_idx, last_profile_idx, -f32::INFINITY);
[INFO] [stdout]     |                   ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:115:19
[INFO] [stdout]     |
[INFO] [stdout] 115 |         dp_matrix.set_delete(
[INFO] [stdout]     |                   ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:119:27
[INFO] [stdout]     |
[INFO] [stdout] 119 |                 dp_matrix.get_match(target_idx, last_profile_idx - 1)
[INFO] [stdout]     |                           ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:120:31
[INFO] [stdout]     |
[INFO] [stdout] 120 |                     + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, last_profile_idx - 1),
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_DELETE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:120:57
[INFO] [stdout]     |
[INFO] [stdout] 120 |                     + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, last_profile_idx - 1),
[INFO] [stdout]     |                                                         ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:121:27
[INFO] [stdout]     |
[INFO] [stdout] 121 |                 dp_matrix.get_delete(target_idx, last_profile_idx - 1)
[INFO] [stdout]     |                           ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:122:31
[INFO] [stdout]     |
[INFO] [stdout] 122 |                     + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, last_profile_idx - 1)
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::DELETE_TO_DELETE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:122:57
[INFO] [stdout]     |
[INFO] [stdout] 122 |                     + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, last_profile_idx - 1)
[INFO] [stdout]     |                                                         ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:127:19
[INFO] [stdout]     |
[INFO] [stdout] 127 |         dp_matrix.set_special(
[INFO] [stdout]     |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:129:22
[INFO] [stdout]     |
[INFO] [stdout] 129 |             Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:131:27
[INFO] [stdout]     |
[INFO] [stdout] 131 |                 dp_matrix.get_match(target_idx, last_profile_idx),
[INFO] [stdout]     |                           ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:132:27
[INFO] [stdout]     |
[INFO] [stdout] 132 |                 dp_matrix.get_delete(target_idx, last_profile_idx),
[INFO] [stdout]     |                           ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:133:27
[INFO] [stdout]     |
[INFO] [stdout] 133 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:133:60
[INFO] [stdout]     |
[INFO] [stdout] 133 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:138:19
[INFO] [stdout]     |
[INFO] [stdout] 138 |         dp_matrix.set_special(
[INFO] [stdout]     |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:140:22
[INFO] [stdout]     |
[INFO] [stdout] 140 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:142:27
[INFO] [stdout]     |
[INFO] [stdout] 142 |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:142:64
[INFO] [stdout]     |
[INFO] [stdout] 142 |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                                ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:143:31
[INFO] [stdout]     |
[INFO] [stdout] 143 |                     + profile.special_transition_score(
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:144:34
[INFO] [stdout]     |
[INFO] [stdout] 144 |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:145:34
[INFO] [stdout]     |
[INFO] [stdout] 145 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:147:27
[INFO] [stdout]     |
[INFO] [stdout] 147 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:147:60
[INFO] [stdout]     |
[INFO] [stdout] 147 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:148:31
[INFO] [stdout]     |
[INFO] [stdout] 148 |                     + profile.special_transition_score(
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:149:34
[INFO] [stdout]     |
[INFO] [stdout] 149 |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:150:34
[INFO] [stdout]     |
[INFO] [stdout] 150 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:156:19
[INFO] [stdout]     |
[INFO] [stdout] 156 |         dp_matrix.set_special(
[INFO] [stdout]     |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:158:22
[INFO] [stdout]     |
[INFO] [stdout] 158 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:160:27
[INFO] [stdout]     |
[INFO] [stdout] 160 |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:160:64
[INFO] [stdout]     |
[INFO] [stdout] 160 |                 dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                                ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:161:31
[INFO] [stdout]     |
[INFO] [stdout] 161 |                     + profile.special_transition_score(
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:162:34
[INFO] [stdout]     |
[INFO] [stdout] 162 |                         Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:163:34
[INFO] [stdout]     |
[INFO] [stdout] 163 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:165:27
[INFO] [stdout]     |
[INFO] [stdout] 165 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:165:60
[INFO] [stdout]     |
[INFO] [stdout] 165 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:166:31
[INFO] [stdout]     |
[INFO] [stdout] 166 |                     + profile.special_transition_score(
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:167:34
[INFO] [stdout]     |
[INFO] [stdout] 167 |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_MOVE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:168:34
[INFO] [stdout]     |
[INFO] [stdout] 168 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:174:19
[INFO] [stdout]     |
[INFO] [stdout] 174 |         dp_matrix.set_special(
[INFO] [stdout]     |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:176:22
[INFO] [stdout]     |
[INFO] [stdout] 176 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:177:23
[INFO] [stdout]     |
[INFO] [stdout] 177 |             dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                       ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:177:60
[INFO] [stdout]     |
[INFO] [stdout] 177 |             dp_matrix.get_special(target_idx - 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:179:22
[INFO] [stdout]     |
[INFO] [stdout] 179 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                      ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:179:56
[INFO] [stdout]     |
[INFO] [stdout] 179 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:179:80
[INFO] [stdout]     |
[INFO] [stdout] 179 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                                                                ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:183:19
[INFO] [stdout]     |
[INFO] [stdout] 183 |         dp_matrix.set_special(
[INFO] [stdout]     |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:185:22
[INFO] [stdout]     |
[INFO] [stdout] 185 |             Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:187:27
[INFO] [stdout]     |
[INFO] [stdout] 187 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:187:60
[INFO] [stdout]     |
[INFO] [stdout] 187 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:188:31
[INFO] [stdout]     |
[INFO] [stdout] 188 |                     + profile.special_transition_score(
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:189:34
[INFO] [stdout]     |
[INFO] [stdout] 189 |                         Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_MOVE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:190:34
[INFO] [stdout]     |
[INFO] [stdout] 190 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:192:27
[INFO] [stdout]     |
[INFO] [stdout] 192 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:192:60
[INFO] [stdout]     |
[INFO] [stdout] 192 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:193:31
[INFO] [stdout]     |
[INFO] [stdout] 193 |                     + profile.special_transition_score(
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:194:34
[INFO] [stdout]     |
[INFO] [stdout] 194 |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_MOVE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:195:34
[INFO] [stdout]     |
[INFO] [stdout] 195 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:201:15
[INFO] [stdout]     |
[INFO] [stdout] 201 |     dp_matrix.get_special(bounds.target_end, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/forward_bounded.rs:201:55
[INFO] [stdout]     |
[INFO] [stdout] 201 |     dp_matrix.get_special(bounds.target_end, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                       ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:39:15
[INFO] [stdout]    |
[INFO] [stdout] 39 |     dp_matrix.set_special(
[INFO] [stdout]    |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:41:18
[INFO] [stdout]    |
[INFO] [stdout] 41 |         Profile::SPECIAL_J_IDX,
[INFO] [stdout]    |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:44:15
[INFO] [stdout]    |
[INFO] [stdout] 44 |     dp_matrix.set_special(
[INFO] [stdout]    |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:46:18
[INFO] [stdout]    |
[INFO] [stdout] 46 |         Profile::SPECIAL_B_IDX,
[INFO] [stdout]    |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:49:15
[INFO] [stdout]    |
[INFO] [stdout] 49 |     dp_matrix.set_special(
[INFO] [stdout]    |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:51:18
[INFO] [stdout]    |
[INFO] [stdout] 51 |         Profile::SPECIAL_N_IDX,
[INFO] [stdout]    |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:55:15
[INFO] [stdout]    |
[INFO] [stdout] 55 |     dp_matrix.set_special(
[INFO] [stdout]    |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:57:18
[INFO] [stdout]    |
[INFO] [stdout] 57 |         Profile::SPECIAL_C_IDX,
[INFO] [stdout]    |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:58:17
[INFO] [stdout]    |
[INFO] [stdout] 58 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                 ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:58:51
[INFO] [stdout]    |
[INFO] [stdout] 58 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                   ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_MOVE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:58:75
[INFO] [stdout]    |
[INFO] [stdout] 58 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                                           ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:61:15
[INFO] [stdout]    |
[INFO] [stdout] 61 |     dp_matrix.set_special(
[INFO] [stdout]    |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:63:18
[INFO] [stdout]    |
[INFO] [stdout] 63 |         Profile::SPECIAL_E_IDX,
[INFO] [stdout]    |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:64:17
[INFO] [stdout]    |
[INFO] [stdout] 64 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]    |                 ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:64:51
[INFO] [stdout]    |
[INFO] [stdout] 64 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]    |                                                   ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_MOVE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:64:75
[INFO] [stdout]    |
[INFO] [stdout] 64 |         profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]    |                                                                           ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:65:23
[INFO] [stdout]    |
[INFO] [stdout] 65 |             + profile.special_transition_score(Profile::SPECIAL_E_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                       ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:65:57
[INFO] [stdout]    |
[INFO] [stdout] 65 |             + profile.special_transition_score(Profile::SPECIAL_E_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                         ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_MOVE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:65:81
[INFO] [stdout]    |
[INFO] [stdout] 65 |             + profile.special_transition_score(Profile::SPECIAL_E_IDX, Profile::SPECIAL_MOVE_IDX),
[INFO] [stdout]    |                                                                                 ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:82:15
[INFO] [stdout]    |
[INFO] [stdout] 82 |     dp_matrix.set_match(
[INFO] [stdout]    |               ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:85:19
[INFO] [stdout]    |
[INFO] [stdout] 85 |         dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX),
[INFO] [stdout]    |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:85:63
[INFO] [stdout]    |
[INFO] [stdout] 85 |         dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX),
[INFO] [stdout]    |                                                               ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:88:15
[INFO] [stdout]    |
[INFO] [stdout] 88 |     dp_matrix.set_delete(
[INFO] [stdout]    |               ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:91:19
[INFO] [stdout]    |
[INFO] [stdout] 91 |         dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX),
[INFO] [stdout]    |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:91:63
[INFO] [stdout]    |
[INFO] [stdout] 91 |         dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX),
[INFO] [stdout]    |                                                               ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/backward_bounded.rs:94:15
[INFO] [stdout]    |
[INFO] [stdout] 94 |     dp_matrix.set_insert(
[INFO] [stdout]    |               ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:113:19
[INFO] [stdout]     |
[INFO] [stdout] 113 |         dp_matrix.set_match(
[INFO] [stdout]     |                   ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:117:27
[INFO] [stdout]     |
[INFO] [stdout] 117 |                 dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:117:71
[INFO] [stdout]     |
[INFO] [stdout] 117 |                 dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]     |                                                                       ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:118:27
[INFO] [stdout]     |
[INFO] [stdout] 118 |                 dp_matrix.get_delete(row_bounds.target_end, profile_idx + 1)
[INFO] [stdout]     |                           ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:119:31
[INFO] [stdout]     |
[INFO] [stdout] 119 |                     + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_DELETE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:119:57
[INFO] [stdout]     |
[INFO] [stdout] 119 |                     + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]     |                                                         ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:123:19
[INFO] [stdout]     |
[INFO] [stdout] 123 |         dp_matrix.set_insert(row_bounds.target_end, profile_idx, -f32::INFINITY);
[INFO] [stdout]     |                   ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:124:19
[INFO] [stdout]     |
[INFO] [stdout] 124 |         dp_matrix.set_delete(
[INFO] [stdout]     |                   ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:128:27
[INFO] [stdout]     |
[INFO] [stdout] 128 |                 dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:128:71
[INFO] [stdout]     |
[INFO] [stdout] 128 |                 dp_matrix.get_special(row_bounds.target_end, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]     |                                                                       ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:129:27
[INFO] [stdout]     |
[INFO] [stdout] 129 |                 dp_matrix.get_delete(row_bounds.target_end, profile_idx + 1)
[INFO] [stdout]     |                           ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:130:31
[INFO] [stdout]     |
[INFO] [stdout] 130 |                     + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::DELETE_TO_DELETE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:130:57
[INFO] [stdout]     |
[INFO] [stdout] 130 |                     + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]     |                                                         ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `structs::sequence::Sequence::digital_bytes`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:137:31
[INFO] [stdout]     |
[INFO] [stdout] 137 |         let current_residue = target.digital_bytes[target_idx + 1] as usize;
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:159:19
[INFO] [stdout]     |
[INFO] [stdout] 159 |         dp_matrix.set_special(
[INFO] [stdout]     |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:161:22
[INFO] [stdout]     |
[INFO] [stdout] 161 |             Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:162:23
[INFO] [stdout]     |
[INFO] [stdout] 162 |             dp_matrix.get_match(target_idx + 1, profile_start_on_current_row)
[INFO] [stdout]     |                       ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:163:27
[INFO] [stdout]     |
[INFO] [stdout] 163 |                 + profile.transition_score(
[INFO] [stdout]     |                           ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::BEGIN_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:164:30
[INFO] [stdout]     |
[INFO] [stdout] 164 |                     Profile::BEGIN_TO_MATCH_IDX,
[INFO] [stdout]     |                              ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::match_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:167:27
[INFO] [stdout]     |
[INFO] [stdout] 167 |                 + profile.match_score(current_residue, profile_start_on_current_row),
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:173:23
[INFO] [stdout]     |
[INFO] [stdout] 173 |             dp_matrix.set_special(
[INFO] [stdout]     |                       ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:175:26
[INFO] [stdout]     |
[INFO] [stdout] 175 |                 Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |                          ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:177:31
[INFO] [stdout]     |
[INFO] [stdout] 177 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX),
[INFO] [stdout]     |                               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:177:64
[INFO] [stdout]     |
[INFO] [stdout] 177 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX),
[INFO] [stdout]     |                                                                ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:178:31
[INFO] [stdout]     |
[INFO] [stdout] 178 |                     dp_matrix.get_match(target_idx + 1, profile_idx)
[INFO] [stdout]     |                               ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:179:35
[INFO] [stdout]     |
[INFO] [stdout] 179 |                         + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]     |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::BEGIN_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:179:61
[INFO] [stdout]     |
[INFO] [stdout] 179 |                         + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]     |                                                             ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::match_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:180:35
[INFO] [stdout]     |
[INFO] [stdout] 180 |                         + profile.match_score(current_residue, profile_idx)
[INFO] [stdout]     |                                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:185:19
[INFO] [stdout]     |
[INFO] [stdout] 185 |         dp_matrix.set_special(
[INFO] [stdout]     |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:187:22
[INFO] [stdout]     |
[INFO] [stdout] 187 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:189:27
[INFO] [stdout]     |
[INFO] [stdout] 189 |                 dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:189:64
[INFO] [stdout]     |
[INFO] [stdout] 189 |                 dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                                ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:190:31
[INFO] [stdout]     |
[INFO] [stdout] 190 |                     + profile.special_transition_score(
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:191:34
[INFO] [stdout]     |
[INFO] [stdout] 191 |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:192:34
[INFO] [stdout]     |
[INFO] [stdout] 192 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:194:27
[INFO] [stdout]     |
[INFO] [stdout] 194 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:194:60
[INFO] [stdout]     |
[INFO] [stdout] 194 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:195:31
[INFO] [stdout]     |
[INFO] [stdout] 195 |                     + profile.special_transition_score(
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:196:34
[INFO] [stdout]     |
[INFO] [stdout] 196 |                         Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_MOVE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:197:34
[INFO] [stdout]     |
[INFO] [stdout] 197 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:202:19
[INFO] [stdout]     |
[INFO] [stdout] 202 |         dp_matrix.set_special(
[INFO] [stdout]     |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:204:22
[INFO] [stdout]     |
[INFO] [stdout] 204 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:205:23
[INFO] [stdout]     |
[INFO] [stdout] 205 |             dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                       ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:205:60
[INFO] [stdout]     |
[INFO] [stdout] 205 |             dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:207:22
[INFO] [stdout]     |
[INFO] [stdout] 207 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                      ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:207:56
[INFO] [stdout]     |
[INFO] [stdout] 207 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:207:80
[INFO] [stdout]     |
[INFO] [stdout] 207 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                                                                ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:210:19
[INFO] [stdout]     |
[INFO] [stdout] 210 |         dp_matrix.set_special(
[INFO] [stdout]     |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:212:22
[INFO] [stdout]     |
[INFO] [stdout] 212 |             Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:214:27
[INFO] [stdout]     |
[INFO] [stdout] 214 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:214:60
[INFO] [stdout]     |
[INFO] [stdout] 214 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:215:31
[INFO] [stdout]     |
[INFO] [stdout] 215 |                     + profile.special_transition_score(
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:216:34
[INFO] [stdout]     |
[INFO] [stdout] 216 |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:217:34
[INFO] [stdout]     |
[INFO] [stdout] 217 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:219:27
[INFO] [stdout]     |
[INFO] [stdout] 219 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:219:60
[INFO] [stdout]     |
[INFO] [stdout] 219 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:220:31
[INFO] [stdout]     |
[INFO] [stdout] 220 |                     + profile.special_transition_score(
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:221:34
[INFO] [stdout]     |
[INFO] [stdout] 221 |                         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_MOVE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:222:34
[INFO] [stdout]     |
[INFO] [stdout] 222 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:227:19
[INFO] [stdout]     |
[INFO] [stdout] 227 |         dp_matrix.set_special(
[INFO] [stdout]     |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:229:22
[INFO] [stdout]     |
[INFO] [stdout] 229 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:231:27
[INFO] [stdout]     |
[INFO] [stdout] 231 |                 dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:231:64
[INFO] [stdout]     |
[INFO] [stdout] 231 |                 dp_matrix.get_special(target_idx + 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                                ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:232:31
[INFO] [stdout]     |
[INFO] [stdout] 232 |                     + profile.special_transition_score(
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:233:34
[INFO] [stdout]     |
[INFO] [stdout] 233 |                         Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:234:34
[INFO] [stdout]     |
[INFO] [stdout] 234 |                         Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:236:27
[INFO] [stdout]     |
[INFO] [stdout] 236 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:236:60
[INFO] [stdout]     |
[INFO] [stdout] 236 |                 dp_matrix.get_special(target_idx, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:237:31
[INFO] [stdout]     |
[INFO] [stdout] 237 |                     + profile.special_transition_score(
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:238:34
[INFO] [stdout]     |
[INFO] [stdout] 238 |                         Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_MOVE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:239:34
[INFO] [stdout]     |
[INFO] [stdout] 239 |                         Profile::SPECIAL_MOVE_IDX
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:244:19
[INFO] [stdout]     |
[INFO] [stdout] 244 |         dp_matrix.set_match(
[INFO] [stdout]     |                   ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:247:23
[INFO] [stdout]     |
[INFO] [stdout] 247 |             dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                       ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:247:56
[INFO] [stdout]     |
[INFO] [stdout] 247 |             dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:250:19
[INFO] [stdout]     |
[INFO] [stdout] 250 |         dp_matrix.set_insert(target_idx, profile_end_on_current_row, -f32::INFINITY);
[INFO] [stdout]     |                   ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:252:19
[INFO] [stdout]     |
[INFO] [stdout] 252 |         dp_matrix.set_delete(
[INFO] [stdout]     |                   ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:255:23
[INFO] [stdout]     |
[INFO] [stdout] 255 |             dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                       ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:255:56
[INFO] [stdout]     |
[INFO] [stdout] 255 |             dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:259:23
[INFO] [stdout]     |
[INFO] [stdout] 259 |             dp_matrix.set_match(
[INFO] [stdout]     |                       ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:263:31
[INFO] [stdout]     |
[INFO] [stdout] 263 |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout]     |                               ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:264:35
[INFO] [stdout]     |
[INFO] [stdout] 264 |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]     |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:264:61
[INFO] [stdout]     |
[INFO] [stdout] 264 |                         + profile.transition_score(Profile::MATCH_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]     |                                                             ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::match_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:265:35
[INFO] [stdout]     |
[INFO] [stdout] 265 |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout]     |                                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:266:31
[INFO] [stdout]     |
[INFO] [stdout] 266 |                     dp_matrix.get_insert(target_idx + 1, profile_idx)
[INFO] [stdout]     |                               ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:267:35
[INFO] [stdout]     |
[INFO] [stdout] 267 |                         + profile.transition_score(Profile::MATCH_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]     |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_INSERT_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:267:61
[INFO] [stdout]     |
[INFO] [stdout] 267 |                         + profile.transition_score(Profile::MATCH_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]     |                                                             ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::insert_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:268:35
[INFO] [stdout]     |
[INFO] [stdout] 268 |                         + profile.insert_score(current_residue, profile_idx),
[INFO] [stdout]     |                                   ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:269:31
[INFO] [stdout]     |
[INFO] [stdout] 269 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]     |                               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:269:64
[INFO] [stdout]     |
[INFO] [stdout] 269 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX) + end_score,
[INFO] [stdout]     |                                                                ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:270:31
[INFO] [stdout]     |
[INFO] [stdout] 270 |                     dp_matrix.get_delete(target_idx, profile_idx + 1)
[INFO] [stdout]     |                               ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:271:35
[INFO] [stdout]     |
[INFO] [stdout] 271 |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]     |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_DELETE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:271:61
[INFO] [stdout]     |
[INFO] [stdout] 271 |                         + profile.transition_score(Profile::MATCH_TO_DELETE_IDX, profile_idx)
[INFO] [stdout]     |                                                             ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:275:23
[INFO] [stdout]     |
[INFO] [stdout] 275 |             dp_matrix.set_insert(
[INFO] [stdout]     |                       ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:279:31
[INFO] [stdout]     |
[INFO] [stdout] 279 |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout]     |                               ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:280:35
[INFO] [stdout]     |
[INFO] [stdout] 280 |                         + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]     |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::INSERT_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:280:61
[INFO] [stdout]     |
[INFO] [stdout] 280 |                         + profile.transition_score(Profile::INSERT_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]     |                                                             ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::match_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:281:35
[INFO] [stdout]     |
[INFO] [stdout] 281 |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout]     |                                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:282:31
[INFO] [stdout]     |
[INFO] [stdout] 282 |                     dp_matrix.get_insert(target_idx + 1, profile_idx)
[INFO] [stdout]     |                               ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:283:35
[INFO] [stdout]     |
[INFO] [stdout] 283 |                         + profile.transition_score(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]     |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::INSERT_TO_INSERT_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:283:61
[INFO] [stdout]     |
[INFO] [stdout] 283 |                         + profile.transition_score(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]     |                                                             ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::insert_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:284:35
[INFO] [stdout]     |
[INFO] [stdout] 284 |                         + profile.insert_score(current_residue, profile_idx)
[INFO] [stdout]     |                                   ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:288:23
[INFO] [stdout]     |
[INFO] [stdout] 288 |             dp_matrix.set_delete(
[INFO] [stdout]     |                       ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:292:31
[INFO] [stdout]     |
[INFO] [stdout] 292 |                     dp_matrix.get_match(target_idx + 1, profile_idx + 1)
[INFO] [stdout]     |                               ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:293:35
[INFO] [stdout]     |
[INFO] [stdout] 293 |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]     |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::DELETE_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:293:61
[INFO] [stdout]     |
[INFO] [stdout] 293 |                         + profile.transition_score(Profile::DELETE_TO_MATCH_IDX, profile_idx)
[INFO] [stdout]     |                                                             ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::match_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:294:35
[INFO] [stdout]     |
[INFO] [stdout] 294 |                         + profile.match_score(current_residue, profile_idx + 1),
[INFO] [stdout]     |                                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:295:31
[INFO] [stdout]     |
[INFO] [stdout] 295 |                     dp_matrix.get_delete(target_idx, profile_idx + 1)
[INFO] [stdout]     |                               ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:296:35
[INFO] [stdout]     |
[INFO] [stdout] 296 |                         + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx),
[INFO] [stdout]     |                                   ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::DELETE_TO_DELETE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:296:61
[INFO] [stdout]     |
[INFO] [stdout] 296 |                         + profile.transition_score(Profile::DELETE_TO_DELETE_IDX, profile_idx),
[INFO] [stdout]     |                                                             ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:297:31
[INFO] [stdout]     |
[INFO] [stdout] 297 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX) + end_score
[INFO] [stdout]     |                               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:297:64
[INFO] [stdout]     |
[INFO] [stdout] 297 |                     dp_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX) + end_score
[INFO] [stdout]     |                                                                ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated field `structs::sequence::Sequence::digital_bytes`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:303:34
[INFO] [stdout]     |
[INFO] [stdout] 303 |     let first_target_character = target.digital_bytes[row_bounds.target_start] as usize;
[INFO] [stdout]     |                                  ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:308:15
[INFO] [stdout]     |
[INFO] [stdout] 308 |     dp_matrix.set_special(
[INFO] [stdout]     |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:310:18
[INFO] [stdout]     |
[INFO] [stdout] 310 |         Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:311:19
[INFO] [stdout]     |
[INFO] [stdout] 311 |         dp_matrix.get_match(row_bounds.target_start, profile_start_in_first_row)
[INFO] [stdout]     |                   ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:312:23
[INFO] [stdout]     |
[INFO] [stdout] 312 |             + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, 0)
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::BEGIN_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:312:49
[INFO] [stdout]     |
[INFO] [stdout] 312 |             + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, 0)
[INFO] [stdout]     |                                                 ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::match_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:313:23
[INFO] [stdout]     |
[INFO] [stdout] 313 |             + profile.match_score(first_target_character, 1),
[INFO] [stdout]     |                       ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:317:19
[INFO] [stdout]     |
[INFO] [stdout] 317 |         dp_matrix.set_special(
[INFO] [stdout]     |                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:319:22
[INFO] [stdout]     |
[INFO] [stdout] 319 |             Profile::SPECIAL_B_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:321:27
[INFO] [stdout]     |
[INFO] [stdout] 321 |                 dp_matrix.get_special(row_bounds.target_start - 1, Profile::SPECIAL_B_IDX),
[INFO] [stdout]     |                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:321:77
[INFO] [stdout]     |
[INFO] [stdout] 321 |                 dp_matrix.get_special(row_bounds.target_start - 1, Profile::SPECIAL_B_IDX),
[INFO] [stdout]     |                                                                             ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:322:27
[INFO] [stdout]     |
[INFO] [stdout] 322 |                 dp_matrix.get_match(row_bounds.target_start, profile_idx)
[INFO] [stdout]     |                           ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:323:31
[INFO] [stdout]     |
[INFO] [stdout] 323 |                     + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::BEGIN_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:323:57
[INFO] [stdout]     |
[INFO] [stdout] 323 |                     + profile.transition_score(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]     |                                                         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::match_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:324:31
[INFO] [stdout]     |
[INFO] [stdout] 324 |                     + profile.match_score(first_target_character, profile_idx)
[INFO] [stdout]     |                               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:329:15
[INFO] [stdout]     |
[INFO] [stdout] 329 |     dp_matrix.set_special(
[INFO] [stdout]     |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:331:18
[INFO] [stdout]     |
[INFO] [stdout] 331 |         Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:334:15
[INFO] [stdout]     |
[INFO] [stdout] 334 |     dp_matrix.set_special(
[INFO] [stdout]     |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:336:18
[INFO] [stdout]     |
[INFO] [stdout] 336 |         Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:339:15
[INFO] [stdout]     |
[INFO] [stdout] 339 |     dp_matrix.set_special(
[INFO] [stdout]     |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:341:18
[INFO] [stdout]     |
[INFO] [stdout] 341 |         Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:344:15
[INFO] [stdout]     |
[INFO] [stdout] 344 |     dp_matrix.set_special(
[INFO] [stdout]     |               ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:346:18
[INFO] [stdout]     |
[INFO] [stdout] 346 |         Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:348:23
[INFO] [stdout]     |
[INFO] [stdout] 348 |             dp_matrix.get_special(row_bounds.target_start, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                       ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:348:69
[INFO] [stdout]     |
[INFO] [stdout] 348 |             dp_matrix.get_special(row_bounds.target_start, Profile::SPECIAL_N_IDX)
[INFO] [stdout]     |                                                                     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:350:22
[INFO] [stdout]     |
[INFO] [stdout] 350 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                      ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:350:56
[INFO] [stdout]     |
[INFO] [stdout] 350 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:350:80
[INFO] [stdout]     |
[INFO] [stdout] 350 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX),
[INFO] [stdout]     |                                                                                ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:351:23
[INFO] [stdout]     |
[INFO] [stdout] 351 |             dp_matrix.get_special(row_bounds.target_start - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                       ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:351:73
[INFO] [stdout]     |
[INFO] [stdout] 351 |             dp_matrix.get_special(row_bounds.target_start - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                                                         ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:353:22
[INFO] [stdout]     |
[INFO] [stdout] 353 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]     |                      ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:353:56
[INFO] [stdout]     |
[INFO] [stdout] 353 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]     |                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_MOVE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:353:80
[INFO] [stdout]     |
[INFO] [stdout] 353 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_MOVE_IDX)
[INFO] [stdout]     |                                                                                ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:357:19
[INFO] [stdout]     |
[INFO] [stdout] 357 |         dp_matrix.set_match(row_bounds.target_start - 1, profile_idx, -f32::INFINITY);
[INFO] [stdout]     |                   ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:358:19
[INFO] [stdout]     |
[INFO] [stdout] 358 |         dp_matrix.set_insert(row_bounds.target_start - 1, profile_idx, -f32::INFINITY);
[INFO] [stdout]     |                   ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/backward_bounded.rs:359:19
[INFO] [stdout]     |
[INFO] [stdout] 359 |         dp_matrix.set_delete(row_bounds.target_start - 1, profile_idx, -f32::INFINITY);
[INFO] [stdout]     |                   ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:13:10
[INFO] [stdout]    |
[INFO] [stdout] 13 |         .get_special(row_bounds.target_end, Profile::SPECIAL_C_IDX)
[INFO] [stdout]    |          ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:13:54
[INFO] [stdout]    |
[INFO] [stdout] 13 |         .get_special(row_bounds.target_end, Profile::SPECIAL_C_IDX)
[INFO] [stdout]    |                                                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:14:19
[INFO] [stdout]    |
[INFO] [stdout] 14 |         + profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX);
[INFO] [stdout]    |                   ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:14:53
[INFO] [stdout]    |
[INFO] [stdout] 14 |         + profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX);
[INFO] [stdout]    |                                                     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_MOVE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:14:77
[INFO] [stdout]    |
[INFO] [stdout] 14 |         + profile.special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_MOVE_IDX);
[INFO] [stdout]    |                                                                             ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:18:22
[INFO] [stdout]    |
[INFO] [stdout] 18 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_E_IDX, 0.0);
[INFO] [stdout]    |                      ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:18:72
[INFO] [stdout]    |
[INFO] [stdout] 18 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_E_IDX, 0.0);
[INFO] [stdout]    |                                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:19:22
[INFO] [stdout]    |
[INFO] [stdout] 19 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_N_IDX, 0.0);
[INFO] [stdout]    |                      ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:19:72
[INFO] [stdout]    |
[INFO] [stdout] 19 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_N_IDX, 0.0);
[INFO] [stdout]    |                                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:20:22
[INFO] [stdout]    |
[INFO] [stdout] 20 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_J_IDX, 0.0);
[INFO] [stdout]    |                      ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:20:72
[INFO] [stdout]    |
[INFO] [stdout] 20 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_J_IDX, 0.0);
[INFO] [stdout]    |                                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:21:22
[INFO] [stdout]    |
[INFO] [stdout] 21 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_B_IDX, 0.0);
[INFO] [stdout]    |                      ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:21:72
[INFO] [stdout]    |
[INFO] [stdout] 21 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_B_IDX, 0.0);
[INFO] [stdout]    |                                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:22:22
[INFO] [stdout]    |
[INFO] [stdout] 22 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_C_IDX, 0.0);
[INFO] [stdout]    |                      ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:22:72
[INFO] [stdout]    |
[INFO] [stdout] 22 |     posterior_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_C_IDX, 0.0);
[INFO] [stdout]    |                                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:28:26
[INFO] [stdout]    |
[INFO] [stdout] 28 |         posterior_matrix.set_match(row_bounds.target_start - 1, profile_idx, 0.0);
[INFO] [stdout]    |                          ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:29:26
[INFO] [stdout]    |
[INFO] [stdout] 29 |         posterior_matrix.set_insert(row_bounds.target_start - 1, profile_idx, 0.0);
[INFO] [stdout]    |                          ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:30:26
[INFO] [stdout]    |
[INFO] [stdout] 30 |         posterior_matrix.set_delete(row_bounds.target_start - 1, profile_idx, 0.0);
[INFO] [stdout]    |                          ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:39:26
[INFO] [stdout]    |
[INFO] [stdout] 39 |         posterior_matrix.set_match(target_idx, profile_start_in_current_row - 1, 0.0);
[INFO] [stdout]    |                          ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:40:26
[INFO] [stdout]    |
[INFO] [stdout] 40 |         posterior_matrix.set_insert(target_idx, profile_start_in_current_row - 1, 0.0);
[INFO] [stdout]    |                          ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:41:26
[INFO] [stdout]    |
[INFO] [stdout] 41 |         posterior_matrix.set_delete(target_idx, profile_start_in_current_row - 1, 0.0);
[INFO] [stdout]    |                          ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:44:30
[INFO] [stdout]    |
[INFO] [stdout] 44 |             posterior_matrix.set_match(
[INFO] [stdout]    |                              ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:47:33
[INFO] [stdout]    |
[INFO] [stdout] 47 |                 (forward_matrix.get_match(target_idx, profile_idx)
[INFO] [stdout]    |                                 ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:48:39
[INFO] [stdout]    |
[INFO] [stdout] 48 |                     + backward_matrix.get_match(target_idx, profile_idx)
[INFO] [stdout]    |                                       ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:53:45
[INFO] [stdout]    |
[INFO] [stdout] 53 |             denominator += posterior_matrix.get_match(target_idx, profile_idx);
[INFO] [stdout]    |                                             ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:55:30
[INFO] [stdout]    |
[INFO] [stdout] 55 |             posterior_matrix.set_insert(
[INFO] [stdout]    |                              ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:58:33
[INFO] [stdout]    |
[INFO] [stdout] 58 |                 (forward_matrix.get_insert(target_idx, profile_idx)
[INFO] [stdout]    |                                 ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:59:39
[INFO] [stdout]    |
[INFO] [stdout] 59 |                     + backward_matrix.get_insert(target_idx, profile_idx)
[INFO] [stdout]    |                                       ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:64:45
[INFO] [stdout]    |
[INFO] [stdout] 64 |             denominator += posterior_matrix.get_insert(target_idx, profile_idx);
[INFO] [stdout]    |                                             ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:66:30
[INFO] [stdout]    |
[INFO] [stdout] 66 |             posterior_matrix.set_delete(target_idx, profile_idx, 0.0);
[INFO] [stdout]    |                              ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:69:26
[INFO] [stdout]    |
[INFO] [stdout] 69 |         posterior_matrix.set_match(
[INFO] [stdout]    |                          ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:72:29
[INFO] [stdout]    |
[INFO] [stdout] 72 |             (forward_matrix.get_match(target_idx, profile_end_in_current_row)
[INFO] [stdout]    |                             ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:73:35
[INFO] [stdout]    |
[INFO] [stdout] 73 |                 + backward_matrix.get_match(target_idx, profile_end_in_current_row)
[INFO] [stdout]    |                                   ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:78:41
[INFO] [stdout]    |
[INFO] [stdout] 78 |         denominator += posterior_matrix.get_match(target_idx, profile_end_in_current_row);
[INFO] [stdout]    |                                         ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:79:26
[INFO] [stdout]    |
[INFO] [stdout] 79 |         posterior_matrix.set_insert(target_idx, profile_end_in_current_row, 0.0);
[INFO] [stdout]    |                          ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:80:26
[INFO] [stdout]    |
[INFO] [stdout] 80 |         posterior_matrix.set_delete(target_idx, profile_end_in_current_row, 0.0);
[INFO] [stdout]    |                          ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:82:26
[INFO] [stdout]    |
[INFO] [stdout] 82 |         posterior_matrix.set_special(target_idx, Profile::SPECIAL_E_IDX, 0.0);
[INFO] [stdout]    |                          ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:82:59
[INFO] [stdout]    |
[INFO] [stdout] 82 |         posterior_matrix.set_special(target_idx, Profile::SPECIAL_E_IDX, 0.0);
[INFO] [stdout]    |                                                           ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:84:26
[INFO] [stdout]    |
[INFO] [stdout] 84 |         posterior_matrix.set_special(
[INFO] [stdout]    |                          ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:86:22
[INFO] [stdout]    |
[INFO] [stdout] 86 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]    |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:87:29
[INFO] [stdout]    |
[INFO] [stdout] 87 |             (forward_matrix.get_special(target_idx - 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]    |                             ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:87:66
[INFO] [stdout]    |
[INFO] [stdout] 87 |             (forward_matrix.get_special(target_idx - 1, Profile::SPECIAL_N_IDX)
[INFO] [stdout]    |                                                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:88:35
[INFO] [stdout]    |
[INFO] [stdout] 88 |                 + backward_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX)
[INFO] [stdout]    |                                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:88:68
[INFO] [stdout]    |
[INFO] [stdout] 88 |                 + backward_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX)
[INFO] [stdout]    |                                                                    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:90:22
[INFO] [stdout]    |
[INFO] [stdout] 90 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]    |                      ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:90:56
[INFO] [stdout]    |
[INFO] [stdout] 90 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]    |                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:90:80
[INFO] [stdout]    |
[INFO] [stdout] 90 |                     .special_transition_score(Profile::SPECIAL_N_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]    |                                                                                ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:95:26
[INFO] [stdout]    |
[INFO] [stdout] 95 |         posterior_matrix.set_special(
[INFO] [stdout]    |                          ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:97:22
[INFO] [stdout]    |
[INFO] [stdout] 97 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]    |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:98:29
[INFO] [stdout]    |
[INFO] [stdout] 98 |             (forward_matrix.get_special(target_idx - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]    |                             ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:98:66
[INFO] [stdout]    |
[INFO] [stdout] 98 |             (forward_matrix.get_special(target_idx - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]    |                                                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:99:35
[INFO] [stdout]    |
[INFO] [stdout] 99 |                 + backward_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout]    |                                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/posterior_bounded.rs:99:68
[INFO] [stdout]    |
[INFO] [stdout] 99 |                 + backward_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)
[INFO] [stdout]    |                                                                    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:101:22
[INFO] [stdout]     |
[INFO] [stdout] 101 |                     .special_transition_score(Profile::SPECIAL_J_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                      ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:101:56
[INFO] [stdout]     |
[INFO] [stdout] 101 |                     .special_transition_score(Profile::SPECIAL_J_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:101:80
[INFO] [stdout]     |
[INFO] [stdout] 101 |                     .special_transition_score(Profile::SPECIAL_J_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                                                                                ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:106:26
[INFO] [stdout]     |
[INFO] [stdout] 106 |         posterior_matrix.set_special(target_idx, Profile::SPECIAL_B_IDX, 0.0);
[INFO] [stdout]     |                          ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:106:59
[INFO] [stdout]     |
[INFO] [stdout] 106 |         posterior_matrix.set_special(target_idx, Profile::SPECIAL_B_IDX, 0.0);
[INFO] [stdout]     |                                                           ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:108:26
[INFO] [stdout]     |
[INFO] [stdout] 108 |         posterior_matrix.set_special(
[INFO] [stdout]     |                          ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:110:22
[INFO] [stdout]     |
[INFO] [stdout] 110 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:111:29
[INFO] [stdout]     |
[INFO] [stdout] 111 |             (forward_matrix.get_special(target_idx - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                             ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:111:66
[INFO] [stdout]     |
[INFO] [stdout] 111 |             (forward_matrix.get_special(target_idx - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:112:35
[INFO] [stdout]     |
[INFO] [stdout] 112 |                 + backward_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                   ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:112:68
[INFO] [stdout]     |
[INFO] [stdout] 112 |                 + backward_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                                    ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:114:22
[INFO] [stdout]     |
[INFO] [stdout] 114 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                      ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:114:56
[INFO] [stdout]     |
[INFO] [stdout] 114 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                                                        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:114:80
[INFO] [stdout]     |
[INFO] [stdout] 114 |                     .special_transition_score(Profile::SPECIAL_C_IDX, Profile::SPECIAL_LOOP_IDX)
[INFO] [stdout]     |                                                                                ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:119:41
[INFO] [stdout]     |
[INFO] [stdout] 119 |         denominator += posterior_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX);
[INFO] [stdout]     |                                         ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:119:74
[INFO] [stdout]     |
[INFO] [stdout] 119 |         denominator += posterior_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX);
[INFO] [stdout]     |                                                                          ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:120:41
[INFO] [stdout]     |
[INFO] [stdout] 120 |         denominator += posterior_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX);
[INFO] [stdout]     |                                         ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:120:74
[INFO] [stdout]     |
[INFO] [stdout] 120 |         denominator += posterior_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX);
[INFO] [stdout]     |                                                                          ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:121:41
[INFO] [stdout]     |
[INFO] [stdout] 121 |         denominator += posterior_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX);
[INFO] [stdout]     |                                         ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:121:74
[INFO] [stdout]     |
[INFO] [stdout] 121 |         denominator += posterior_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX);
[INFO] [stdout]     |                                                                          ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:126:30
[INFO] [stdout]     |
[INFO] [stdout] 126 |             posterior_matrix.set_match(
[INFO] [stdout]     |                              ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:129:34
[INFO] [stdout]     |
[INFO] [stdout] 129 |                 posterior_matrix.get_match(target_idx, profile_idx) * denominator,
[INFO] [stdout]     |                                  ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:132:30
[INFO] [stdout]     |
[INFO] [stdout] 132 |             posterior_matrix.set_insert(
[INFO] [stdout]     |                              ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:135:34
[INFO] [stdout]     |
[INFO] [stdout] 135 |                 posterior_matrix.get_insert(target_idx, profile_idx) * denominator,
[INFO] [stdout]     |                                  ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:139:26
[INFO] [stdout]     |
[INFO] [stdout] 139 |         posterior_matrix.set_match(
[INFO] [stdout]     |                          ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:142:30
[INFO] [stdout]     |
[INFO] [stdout] 142 |             posterior_matrix.get_match(target_idx, profile_end_in_current_row) * denominator,
[INFO] [stdout]     |                              ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:145:26
[INFO] [stdout]     |
[INFO] [stdout] 145 |         posterior_matrix.set_special(
[INFO] [stdout]     |                          ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:147:22
[INFO] [stdout]     |
[INFO] [stdout] 147 |             Profile::SPECIAL_N_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:148:30
[INFO] [stdout]     |
[INFO] [stdout] 148 |             posterior_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX) * denominator,
[INFO] [stdout]     |                              ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:148:63
[INFO] [stdout]     |
[INFO] [stdout] 148 |             posterior_matrix.get_special(target_idx, Profile::SPECIAL_N_IDX) * denominator,
[INFO] [stdout]     |                                                               ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:151:26
[INFO] [stdout]     |
[INFO] [stdout] 151 |         posterior_matrix.set_special(
[INFO] [stdout]     |                          ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:153:22
[INFO] [stdout]     |
[INFO] [stdout] 153 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:154:30
[INFO] [stdout]     |
[INFO] [stdout] 154 |             posterior_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX) * denominator,
[INFO] [stdout]     |                              ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:154:63
[INFO] [stdout]     |
[INFO] [stdout] 154 |             posterior_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX) * denominator,
[INFO] [stdout]     |                                                               ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:157:26
[INFO] [stdout]     |
[INFO] [stdout] 157 |         posterior_matrix.set_special(
[INFO] [stdout]     |                          ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:159:22
[INFO] [stdout]     |
[INFO] [stdout] 159 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:160:30
[INFO] [stdout]     |
[INFO] [stdout] 160 |             posterior_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX) * denominator,
[INFO] [stdout]     |                              ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/posterior_bounded.rs:160:63
[INFO] [stdout]     |
[INFO] [stdout] 160 |             posterior_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX) * denominator,
[INFO] [stdout]     |                                                               ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:15:20
[INFO] [stdout]    |
[INFO] [stdout] 15 |     optimal_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_N_IDX, 0.0);
[INFO] [stdout]    |                    ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_N_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:15:70
[INFO] [stdout]    |
[INFO] [stdout] 15 |     optimal_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_N_IDX, 0.0);
[INFO] [stdout]    |                                                                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:16:20
[INFO] [stdout]    |
[INFO] [stdout] 16 |     optimal_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_B_IDX, 0.0);
[INFO] [stdout]    |                    ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:16:70
[INFO] [stdout]    |
[INFO] [stdout] 16 |     optimal_matrix.set_special(row_bounds.target_start - 1, Profile::SPECIAL_B_IDX, 0.0);
[INFO] [stdout]    |                                                                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:17:20
[INFO] [stdout]    |
[INFO] [stdout] 17 |     optimal_matrix.set_special(
[INFO] [stdout]    |                    ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:19:18
[INFO] [stdout]    |
[INFO] [stdout] 19 |         Profile::SPECIAL_E_IDX,
[INFO] [stdout]    |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:22:20
[INFO] [stdout]    |
[INFO] [stdout] 22 |     optimal_matrix.set_special(
[INFO] [stdout]    |                    ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:24:18
[INFO] [stdout]    |
[INFO] [stdout] 24 |         Profile::SPECIAL_C_IDX,
[INFO] [stdout]    |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:27:20
[INFO] [stdout]    |
[INFO] [stdout] 27 |     optimal_matrix.set_special(
[INFO] [stdout]    |                    ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:29:18
[INFO] [stdout]    |
[INFO] [stdout] 29 |         Profile::SPECIAL_J_IDX,
[INFO] [stdout]    |                  ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:38:24
[INFO] [stdout]    |
[INFO] [stdout] 38 |         optimal_matrix.set_match(row_bounds.target_start - 1, profile_idx, -f32::INFINITY);
[INFO] [stdout]    |                        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:39:24
[INFO] [stdout]    |
[INFO] [stdout] 39 |         optimal_matrix.set_insert(row_bounds.target_start - 1, profile_idx, -f32::INFINITY);
[INFO] [stdout]    |                        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:40:24
[INFO] [stdout]    |
[INFO] [stdout] 40 |         optimal_matrix.set_delete(row_bounds.target_start - 1, profile_idx, -f32::INFINITY);
[INFO] [stdout]    |                        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:48:24
[INFO] [stdout]    |
[INFO] [stdout] 48 |         optimal_matrix.set_match(target_idx, profile_start_in_current_row - 1, -f32::INFINITY);
[INFO] [stdout]    |                        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:49:24
[INFO] [stdout]    |
[INFO] [stdout] 49 |         optimal_matrix.set_insert(target_idx, profile_start_in_current_row - 1, -f32::INFINITY);
[INFO] [stdout]    |                        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:50:24
[INFO] [stdout]    |
[INFO] [stdout] 50 |         optimal_matrix.set_delete(target_idx, profile_start_in_current_row - 1, -f32::INFINITY);
[INFO] [stdout]    |                        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:51:24
[INFO] [stdout]    |
[INFO] [stdout] 51 |         optimal_matrix.set_special(target_idx, Profile::SPECIAL_E_IDX, -f32::INFINITY);
[INFO] [stdout]    |                        ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:51:57
[INFO] [stdout]    |
[INFO] [stdout] 51 |         optimal_matrix.set_special(target_idx, Profile::SPECIAL_E_IDX, -f32::INFINITY);
[INFO] [stdout]    |                                                         ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:55:28
[INFO] [stdout]    |
[INFO] [stdout] 55 |             optimal_matrix.set_match(
[INFO] [stdout]    |                            ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:59:29
[INFO] [stdout]    |
[INFO] [stdout] 59 |                     profile.transition_score_delta(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                             ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:59:61
[INFO] [stdout]    |
[INFO] [stdout] 59 |                     profile.transition_score_delta(Profile::MATCH_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:60:43
[INFO] [stdout]    |
[INFO] [stdout] 60 |                         * (optimal_matrix.get_match(target_idx - 1, profile_idx - 1)
[INFO] [stdout]    |                                           ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:61:48
[INFO] [stdout]    |
[INFO] [stdout] 61 | ...                   + posterior_matrix.get_match(target_idx, profile_idx)),
[INFO] [stdout]    |                                          ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:62:29
[INFO] [stdout]    |
[INFO] [stdout] 62 |                     profile.transition_score_delta(Profile::INSERT_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                             ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::INSERT_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:62:61
[INFO] [stdout]    |
[INFO] [stdout] 62 |                     profile.transition_score_delta(Profile::INSERT_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:63:43
[INFO] [stdout]    |
[INFO] [stdout] 63 |                         * (optimal_matrix.get_insert(target_idx - 1, profile_idx - 1)
[INFO] [stdout]    |                                           ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:64:48
[INFO] [stdout]    |
[INFO] [stdout] 64 | ...                   + posterior_matrix.get_match(target_idx, profile_idx)),
[INFO] [stdout]    |                                          ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:65:29
[INFO] [stdout]    |
[INFO] [stdout] 65 |                     profile.transition_score_delta(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                             ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::DELETE_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:65:61
[INFO] [stdout]    |
[INFO] [stdout] 65 |                     profile.transition_score_delta(Profile::DELETE_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:66:43
[INFO] [stdout]    |
[INFO] [stdout] 66 |                         * (optimal_matrix.get_delete(target_idx - 1, profile_idx - 1)
[INFO] [stdout]    |                                           ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:67:48
[INFO] [stdout]    |
[INFO] [stdout] 67 | ...                   + posterior_matrix.get_match(target_idx, profile_idx)),
[INFO] [stdout]    |                                          ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:68:29
[INFO] [stdout]    |
[INFO] [stdout] 68 |                     profile.transition_score_delta(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                             ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::BEGIN_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:68:61
[INFO] [stdout]    |
[INFO] [stdout] 68 |                     profile.transition_score_delta(Profile::BEGIN_TO_MATCH_IDX, profile_idx - 1)
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:69:43
[INFO] [stdout]    |
[INFO] [stdout] 69 |                         * (optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]    |                                           ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:69:80
[INFO] [stdout]    |
[INFO] [stdout] 69 |                         * (optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]    |                                                                                ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:70:48
[INFO] [stdout]    |
[INFO] [stdout] 70 | ...                   + posterior_matrix.get_match(target_idx, profile_idx))
[INFO] [stdout]    |                                          ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:74:28
[INFO] [stdout]    |
[INFO] [stdout] 74 |             optimal_matrix.set_special(
[INFO] [stdout]    |                            ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:76:26
[INFO] [stdout]    |
[INFO] [stdout] 76 |                 Profile::SPECIAL_E_IDX,
[INFO] [stdout]    |                          ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:78:36
[INFO] [stdout]    |
[INFO] [stdout] 78 |                     optimal_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]    |                                    ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:78:69
[INFO] [stdout]    |
[INFO] [stdout] 78 |                     optimal_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]    |                                                                     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:79:36
[INFO] [stdout]    |
[INFO] [stdout] 79 |                     optimal_matrix.get_match(target_idx, profile_idx) * end_score
[INFO] [stdout]    |                                    ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:83:28
[INFO] [stdout]    |
[INFO] [stdout] 83 |             optimal_matrix.set_insert(
[INFO] [stdout]    |                            ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:87:29
[INFO] [stdout]    |
[INFO] [stdout] 87 |                     profile.transition_score_delta(Profile::MATCH_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                             ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_INSERT_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:87:61
[INFO] [stdout]    |
[INFO] [stdout] 87 |                     profile.transition_score_delta(Profile::MATCH_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:88:43
[INFO] [stdout]    |
[INFO] [stdout] 88 |                         * (optimal_matrix.get_match(target_idx - 1, profile_idx)
[INFO] [stdout]    |                                           ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:89:48
[INFO] [stdout]    |
[INFO] [stdout] 89 | ...                   + posterior_matrix.get_insert(target_idx, profile_idx)),
[INFO] [stdout]    |                                          ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:90:29
[INFO] [stdout]    |
[INFO] [stdout] 90 |                     profile.transition_score_delta(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                             ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::INSERT_TO_INSERT_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:90:61
[INFO] [stdout]    |
[INFO] [stdout] 90 |                     profile.transition_score_delta(Profile::INSERT_TO_INSERT_IDX, profile_idx)
[INFO] [stdout]    |                                                             ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:91:43
[INFO] [stdout]    |
[INFO] [stdout] 91 |                         * (optimal_matrix.get_insert(target_idx - 1, profile_idx)
[INFO] [stdout]    |                                           ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:92:48
[INFO] [stdout]    |
[INFO] [stdout] 92 | ...                   + posterior_matrix.get_insert(target_idx, profile_idx))
[INFO] [stdout]    |                                          ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]   --> src/align/bounded/optimal_accuracy_bounded.rs:96:28
[INFO] [stdout]    |
[INFO] [stdout] 96 |             optimal_matrix.set_delete(
[INFO] [stdout]    |                            ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:100:29
[INFO] [stdout]     |
[INFO] [stdout] 100 |                     profile.transition_score_delta(Profile::MATCH_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]     |                             ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_DELETE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:100:61
[INFO] [stdout]     |
[INFO] [stdout] 100 |                     profile.transition_score_delta(Profile::MATCH_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]     |                                                             ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:101:42
[INFO] [stdout]     |
[INFO] [stdout] 101 |                         * optimal_matrix.get_match(target_idx, profile_idx - 1),
[INFO] [stdout]     |                                          ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:102:29
[INFO] [stdout]     |
[INFO] [stdout] 102 |                     profile.transition_score_delta(Profile::DELETE_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]     |                             ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::DELETE_TO_DELETE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:102:61
[INFO] [stdout]     |
[INFO] [stdout] 102 |                     profile.transition_score_delta(Profile::DELETE_TO_DELETE_IDX, profile_idx - 1)
[INFO] [stdout]     |                                                             ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:103:42
[INFO] [stdout]     |
[INFO] [stdout] 103 |                         * optimal_matrix.get_delete(target_idx, profile_idx - 1)
[INFO] [stdout]     |                                          ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:108:24
[INFO] [stdout]     |
[INFO] [stdout] 108 |         optimal_matrix.set_match(
[INFO] [stdout]     |                        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:112:25
[INFO] [stdout]     |
[INFO] [stdout] 112 |                 profile.transition_score_delta(
[INFO] [stdout]     |                         ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:113:30
[INFO] [stdout]     |
[INFO] [stdout] 113 |                     Profile::MATCH_TO_MATCH_IDX,
[INFO] [stdout]     |                              ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:115:37
[INFO] [stdout]     |
[INFO] [stdout] 115 |                 ) * (optimal_matrix.get_match(target_idx - 1, profile_end_in_current_row - 1)
[INFO] [stdout]     |                                     ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:116:40
[INFO] [stdout]     |
[INFO] [stdout] 116 |                     + posterior_matrix.get_match(target_idx, profile_end_in_current_row)),
[INFO] [stdout]     |                                        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:117:25
[INFO] [stdout]     |
[INFO] [stdout] 117 |                 profile.transition_score_delta(
[INFO] [stdout]     |                         ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::INSERT_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:118:30
[INFO] [stdout]     |
[INFO] [stdout] 118 |                     Profile::INSERT_TO_MATCH_IDX,
[INFO] [stdout]     |                              ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_insert`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:120:37
[INFO] [stdout]     |
[INFO] [stdout] 120 |                 ) * (optimal_matrix.get_insert(target_idx - 1, profile_end_in_current_row - 1)
[INFO] [stdout]     |                                     ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:121:40
[INFO] [stdout]     |
[INFO] [stdout] 121 |                     + posterior_matrix.get_match(target_idx, profile_end_in_current_row)),
[INFO] [stdout]     |                                        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:122:25
[INFO] [stdout]     |
[INFO] [stdout] 122 |                 profile.transition_score_delta(
[INFO] [stdout]     |                         ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::DELETE_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:123:30
[INFO] [stdout]     |
[INFO] [stdout] 123 |                     Profile::DELETE_TO_MATCH_IDX,
[INFO] [stdout]     |                              ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:125:37
[INFO] [stdout]     |
[INFO] [stdout] 125 |                 ) * (optimal_matrix.get_delete(target_idx - 1, profile_end_in_current_row - 1)
[INFO] [stdout]     |                                     ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:126:40
[INFO] [stdout]     |
[INFO] [stdout] 126 |                     + posterior_matrix.get_match(target_idx, profile_end_in_current_row)),
[INFO] [stdout]     |                                        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:127:25
[INFO] [stdout]     |
[INFO] [stdout] 127 |                 profile.transition_score_delta(
[INFO] [stdout]     |                         ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::BEGIN_TO_MATCH_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:128:30
[INFO] [stdout]     |
[INFO] [stdout] 128 |                     Profile::BEGIN_TO_MATCH_IDX,
[INFO] [stdout]     |                              ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:130:37
[INFO] [stdout]     |
[INFO] [stdout] 130 |                 ) * (optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                     ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_B_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:130:74
[INFO] [stdout]     |
[INFO] [stdout] 130 |                 ) * (optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_B_IDX)
[INFO] [stdout]     |                                                                          ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:131:40
[INFO] [stdout]     |
[INFO] [stdout] 131 |                     + posterior_matrix.get_match(target_idx, profile_end_in_current_row))
[INFO] [stdout]     |                                        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:135:24
[INFO] [stdout]     |
[INFO] [stdout] 135 |         optimal_matrix.set_delete(
[INFO] [stdout]     |                        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:139:25
[INFO] [stdout]     |
[INFO] [stdout] 139 |                 profile.transition_score_delta(
[INFO] [stdout]     |                         ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::MATCH_TO_DELETE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:140:30
[INFO] [stdout]     |
[INFO] [stdout] 140 |                     Profile::MATCH_TO_DELETE_IDX,
[INFO] [stdout]     |                              ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:142:36
[INFO] [stdout]     |
[INFO] [stdout] 142 |                 ) * optimal_matrix.get_match(target_idx, profile_end_in_current_row - 1),
[INFO] [stdout]     |                                    ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:143:25
[INFO] [stdout]     |
[INFO] [stdout] 143 |                 profile.transition_score_delta(
[INFO] [stdout]     |                         ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::DELETE_TO_DELETE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:144:30
[INFO] [stdout]     |
[INFO] [stdout] 144 |                     Profile::DELETE_TO_DELETE_IDX,
[INFO] [stdout]     |                              ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:146:36
[INFO] [stdout]     |
[INFO] [stdout] 146 |                 ) * optimal_matrix.get_delete(target_idx, profile_end_in_current_row - 1)
[INFO] [stdout]     |                                    ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:152:24
[INFO] [stdout]     |
[INFO] [stdout] 152 |         optimal_matrix.set_special(
[INFO] [stdout]     |                        ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:154:22
[INFO] [stdout]     |
[INFO] [stdout] 154 |             Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:156:32
[INFO] [stdout]     |
[INFO] [stdout] 156 |                 optimal_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                                ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:156:65
[INFO] [stdout]     |
[INFO] [stdout] 156 |                 optimal_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX),
[INFO] [stdout]     |                                                                 ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_match`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:157:32
[INFO] [stdout]     |
[INFO] [stdout] 157 |                 optimal_matrix.get_match(target_idx, profile_end_in_current_row),
[INFO] [stdout]     |                                ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_delete`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:158:32
[INFO] [stdout]     |
[INFO] [stdout] 158 |                 optimal_matrix.get_delete(target_idx, profile_end_in_current_row)
[INFO] [stdout]     |                                ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:162:24
[INFO] [stdout]     |
[INFO] [stdout] 162 |         optimal_matrix.set_special(
[INFO] [stdout]     |                        ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:164:22
[INFO] [stdout]     |
[INFO] [stdout] 164 |             Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:166:25
[INFO] [stdout]     |
[INFO] [stdout] 166 |                 profile.special_transition_score_delta(
[INFO] [stdout]     |                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:167:30
[INFO] [stdout]     |
[INFO] [stdout] 167 |                     Profile::SPECIAL_J_IDX,
[INFO] [stdout]     |                              ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:168:30
[INFO] [stdout]     |
[INFO] [stdout] 168 |                     Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                              ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:169:37
[INFO] [stdout]     |
[INFO] [stdout] 169 |                 ) * (optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                     ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:169:74
[INFO] [stdout]     |
[INFO] [stdout] 169 |                 ) * (optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_J_IDX)
[INFO] [stdout]     |                                                                          ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:170:40
[INFO] [stdout]     |
[INFO] [stdout] 170 |                     + posterior_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)),
[INFO] [stdout]     |                                        ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_J_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:170:73
[INFO] [stdout]     |
[INFO] [stdout] 170 |                     + posterior_matrix.get_special(target_idx, Profile::SPECIAL_J_IDX)),
[INFO] [stdout]     |                                                                         ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:171:25
[INFO] [stdout]     |
[INFO] [stdout] 171 |                 profile.special_transition_score_delta(
[INFO] [stdout]     |                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:172:30
[INFO] [stdout]     |
[INFO] [stdout] 172 |                     Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                              ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:173:30
[INFO] [stdout]     |
[INFO] [stdout] 173 |                     Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                              ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:174:36
[INFO] [stdout]     |
[INFO] [stdout] 174 |                 ) * optimal_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                                    ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:174:69
[INFO] [stdout]     |
[INFO] [stdout] 174 |                 ) * optimal_matrix.get_special(target_idx, Profile::SPECIAL_E_IDX)
[INFO] [stdout]     |                                                                     ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::set_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:178:24
[INFO] [stdout]     |
[INFO] [stdout] 178 |         optimal_matrix.set_special(
[INFO] [stdout]     |                        ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:180:22
[INFO] [stdout]     |
[INFO] [stdout] 180 |             Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |                      ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:182:25
[INFO] [stdout]     |
[INFO] [stdout] 182 |                 profile.special_transition_score_delta(
[INFO] [stdout]     |                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:183:30
[INFO] [stdout]     |
[INFO] [stdout] 183 |                     Profile::SPECIAL_C_IDX,
[INFO] [stdout]     |                              ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_LOOP_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:184:30
[INFO] [stdout]     |
[INFO] [stdout] 184 |                     Profile::SPECIAL_LOOP_IDX
[INFO] [stdout]     |                              ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:185:37
[INFO] [stdout]     |
[INFO] [stdout] 185 |                 ) * (optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                     ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:185:74
[INFO] [stdout]     |
[INFO] [stdout] 185 |                 ) * (optimal_matrix.get_special(target_idx - 1, Profile::SPECIAL_C_IDX)
[INFO] [stdout]     |                                                                          ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::dp_matrix::DpMatrix::get_special`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:186:40
[INFO] [stdout]     |
[INFO] [stdout] 186 |                     + posterior_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX)),
[INFO] [stdout]     |                                        ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_C_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:186:73
[INFO] [stdout]     |
[INFO] [stdout] 186 |                     + posterior_matrix.get_special(target_idx, Profile::SPECIAL_C_IDX)),
[INFO] [stdout]     |                                                                         ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated method `structs::profile::Profile::special_transition_score_delta`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:187:25
[INFO] [stdout]     |
[INFO] [stdout] 187 |                 profile.special_transition_score_delta(
[INFO] [stdout]     |                         ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_E_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:188:30
[INFO] [stdout]     |
[INFO] [stdout] 188 |                     Profile::SPECIAL_E_IDX,
[INFO] [stdout]     |                              ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated associated constant `structs::profile::Profile::SPECIAL_MOVE_IDX`: This crate is deprecated. See the readme for more information.
[INFO] [stdout]    --> src/align/bounded/optimal_accuracy_bounded.rs:189:30
[INFO] [stdout]     |
[INFO] [stdout] 189 |                     Profile::SPECIAL_MOVE_IDX
[WARN] too many lines in the log, truncating it
