[INFO] fetching crate nale 0.1.2... [INFO] testing nale-0.1.2 against try#8de4c7234dd9b97c9d76b58671343fdbbc9a433e+target=x86_64-unknown-linux-musl for musl_upgrade_1_2_5_with_libc_patch_0 [INFO] extracting crate nale 0.1.2 into /workspace/builds/worker-3-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-3-tc1/source/Cargo.toml [INFO] validating manifest of crates.io crate nale 0.1.2 on toolchain 8de4c7234dd9b97c9d76b58671343fdbbc9a433e [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "generate-lockfile" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Locking 29 packages to latest compatible versions [INFO] [stderr] Adding phf v0.11.3 (available: v0.12.1) [INFO] [stderr] Adding thiserror v1.0.69 (available: v2.0.12) [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded seq_io v0.3.4 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 9c92e153968316870b7bf8f854460aac16dded5ad8070bdc0025e87905ab84ce [INFO] running `Command { std: "docker" "start" "-a" "9c92e153968316870b7bf8f854460aac16dded5ad8070bdc0025e87905ab84ce", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "9c92e153968316870b7bf8f854460aac16dded5ad8070bdc0025e87905ab84ce", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "9c92e153968316870b7bf8f854460aac16dded5ad8070bdc0025e87905ab84ce", kill_on_drop: false }` [INFO] [stdout] 9c92e153968316870b7bf8f854460aac16dded5ad8070bdc0025e87905ab84ce [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:90999bfc7ae267e83380e433d8e61a7c072ca6729e92edbae886d3423b3a6f4c" "/opt/rustwide/cargo-home/bin/cargo" "+8de4c7234dd9b97c9d76b58671343fdbbc9a433e" "build" "--frozen" "--message-format=json" "--target" "x86_64-unknown-linux-musl", kill_on_drop: false }` [INFO] [stdout] 577f16b5786a6444128974f56329faa922709141fe2331ab806a6e9e33cc7b75 [INFO] running `Command { std: "docker" "start" "-a" "577f16b5786a6444128974f56329faa922709141fe2331ab806a6e9e33cc7b75", kill_on_drop: false }` [INFO] [stderr] Compiling memchr v2.7.5 [INFO] [stderr] Compiling regex-syntax v0.8.5 [INFO] [stderr] Compiling siphasher v1.0.1 [INFO] [stderr] Compiling scoped_threadpool v0.1.9 [INFO] [stderr] Compiling ryu v1.0.20 [INFO] [stderr] Compiling itoa v1.0.15 [INFO] [stderr] Compiling lazy_static v1.5.0 [INFO] [stderr] Compiling serde v1.0.219 [INFO] [stderr] Compiling phf_shared v0.11.3 [INFO] [stderr] Compiling crossbeam-utils v0.8.21 [INFO] [stderr] Compiling anyhow v1.0.98 [INFO] [stderr] Compiling serde_json v1.0.140 [INFO] [stderr] Compiling thiserror v1.0.69 [INFO] [stderr] Compiling syn v2.0.104 [INFO] [stderr] Compiling phf_generator v0.11.3 [INFO] [stderr] Compiling aho-corasick v1.1.3 [INFO] [stderr] Compiling buffer-redux v1.0.2 [INFO] [stderr] Compiling regex-automata v0.4.9 [INFO] [stderr] Compiling serde_derive v1.0.219 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Compiling phf_macros v0.11.3 [INFO] [stderr] Compiling phf v0.11.3 [INFO] [stderr] Compiling regex v1.11.1 [INFO] [stderr] Compiling seq_io v0.3.4 [INFO] [stderr] Compiling nale v0.1.2 (/opt/rustwide/workdir) [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 = 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 = 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, 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, 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[¤t_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 [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [WARN] too many lines in the log, truncating it