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[INFO] [stderr]     Checking gatk-haplotypecaller v0.1.0 (/opt/rustwide/workdir/gatk-haplotypecaller)
[INFO] [stdout] warning: field `unclassified_hint` is never read
[INFO] [stdout]   --> gatk-haplotypecaller/src/hc_profile/mod.rs:55:5
[INFO] [stdout]    |
[INFO] [stdout] 46 | struct ProfileState {
[INFO] [stdout]    |        ------------ field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 55 |     unclassified_hint: bool,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `hap_oriented_denom` is never read
[INFO] [stdout]    --> gatk-haplotypecaller/src/hc_profile/pairhmm.rs:119:9
[INFO] [stdout]     |
[INFO] [stdout] 112 | pub struct PairHmmOccupancy {
[INFO] [stdout]     |            ---------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 119 |     pub hap_oriented_denom: u64,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `PairHmmOccupancy` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `logless_build_transitions` is never used
[INFO] [stdout]    --> gatk-haplotypecaller/src/pairhmm_logless.rs:131:15
[INFO] [stdout]     |
[INFO] [stdout] 131 | pub(crate) fn logless_build_transitions(
[INFO] [stdout]     |               ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `merge_linear_chain` is never used
[INFO] [stdout]    --> gatk-haplotypecaller/src/seq_graph.rs:402:8
[INFO] [stdout]     |
[INFO] [stdout]  90 | impl SeqGraph {
[INFO] [stdout]     | ------------- method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 402 |     fn merge_linear_chain(&mut self, chain: &[usize]) -> bool {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `qual_by_depth_with_rng` is never used
[INFO] [stdout]    --> gatk-haplotypecaller/src/annotator/plugins/qual_by_depth.rs:133:8
[INFO] [stdout]     |
[INFO] [stdout] 133 | pub fn qual_by_depth_with_rng(qual: f64, dp: i32, rng: &mut GatkJavaRng) -> f64 {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `fix_too_high_qd_with_rng` is never used
[INFO] [stdout]    --> gatk-haplotypecaller/src/annotator/plugins/qual_by_depth.rs:192:8
[INFO] [stdout]     |
[INFO] [stdout] 192 | pub fn fix_too_high_qd_with_rng(qd: f64, rng: &mut GatkJavaRng) -> f64 {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Checking gatk-cli v0.1.0 (/opt/rustwide/workdir/gatk-cli)
[INFO] [stdout] warning: unused variable: `covering_gt`
[INFO] [stdout]    --> gatk-haplotypecaller/tests/holdout_6r200_coverage_secondary_overlap.rs:185:9
[INFO] [stdout]     |
[INFO] [stdout] 185 |     let covering_gt = covering_full(&gap_regions, CLOSED_GT);
[INFO] [stdout]     |         ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_covering_gt`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `classify_info_key` is never used
[INFO] [stdout]    --> gatk-haplotypecaller/tests/forensic_6r190_fresh_info_reconnaissance.rs:261:4
[INFO] [stdout]     |
[INFO] [stdout] 261 | fn classify_info_key(j: &Rec, r: &Rec, key: &str) -> &'static str {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Value`
[INFO] [stdout]   --> gatk-haplotypecaller/tests/holdout_6r116_hap_population.rs:21:24
[INFO] [stdout]    |
[INFO] [stdout] 21 | use serde_json::{json, Value};
[INFO] [stdout]    |                        ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `info_f64` is never used
[INFO] [stdout]   --> gatk-haplotypecaller/tests/holdout_6r219_ad_membership.rs:74:4
[INFO] [stdout]    |
[INFO] [stdout] 74 | fn info_f64(info: &[InfoValue], key: &str) -> Option<f64> {
[INFO] [stdout]    |    ^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> gatk-haplotypecaller/tests/forensic_6r77_assembly_graph_divergence.rs:344:21
[INFO] [stdout]     |
[INFO] [stdout] 344 |                 let mut dump_hits = |label: &str, needle: &[u8]| {
[INFO] [stdout]     |                     ----^^^^^^^^^
[INFO] [stdout]     |                     |
[INFO] [stdout]     |                     help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `covering_gt`
[INFO] [stdout]    --> gatk-haplotypecaller/tests/holdout_6r199_cluster_downstream_annotation.rs:187:9
[INFO] [stdout]     |
[INFO] [stdout] 187 |     let covering_gt = covering_full(&gap_regions, CLOSED_GT);
[INFO] [stdout]     |         ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_covering_gt`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `covering_gt`
[INFO] [stdout]    --> gatk-haplotypecaller/tests/holdout_6r201_coverage_cardinality.rs:187:9
[INFO] [stdout]     |
[INFO] [stdout] 187 |     let covering_gt = covering_full(&gap_regions, CLOSED_GT);
[INFO] [stdout]     |         ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_covering_gt`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `GenomePosition`
[INFO] [stdout]   --> gatk-haplotypecaller/tests/holdout_6r196_qual_indel_af_prior.rs:12:83
[INFO] [stdout]    |
[INFO] [stdout] 12 |     try_emit_call_region_variants, AssemblyRegionCallDisposition, CallRegionArgs, GenomePosition,
[INFO] [stdout]    |                                                                                   ^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `info_has` is never used
[INFO] [stdout]   --> gatk-haplotypecaller/tests/forensic_6r198_per_variant_annotation_object.rs:86:4
[INFO] [stdout]    |
[INFO] [stdout] 86 | fn info_has(info: &[InfoValue], key: &str) -> bool {
[INFO] [stdout]    |    ^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `info_has` is never used
[INFO] [stdout]   --> gatk-haplotypecaller/tests/holdout_6r198_per_variant_object.rs:73:4
[INFO] [stdout]    |
[INFO] [stdout] 73 | fn info_has(info: &[InfoValue], key: &str) -> bool {
[INFO] [stdout]    |    ^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> gatk-haplotypecaller/src/rt_first_configured.rs:215:13
[INFO] [stdout]     |
[INFO] [stdout] 215 |         let mut ref_bases = greedy_unique_k25(80);
[INFO] [stdout]     |             ----^^^^^^^^^
[INFO] [stdout]     |             |
[INFO] [stdout]     |             help: remove this `mut`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> gatk-haplotypecaller/src/read_event_discovery/../../tests/discovery/event_discovery_unit.rs:434:9
[INFO] [stdout]     |
[INFO] [stdout] 434 |     let mut fa = rust_htslib::faidx::Reader::from_path(fa_path).expect("fa");
[INFO] [stdout]     |         ----^^
[INFO] [stdout]     |         |
[INFO] [stdout]     |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `rust_alt` and `java_alt` are never read
[INFO] [stdout]    --> gatk-haplotypecaller/src/assembly_dangling_recovery.rs:459:9
[INFO] [stdout]     |
[INFO] [stdout] 442 | pub(crate) struct PathBasesHoldoutRow {
[INFO] [stdout]     |                   ------------------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 459 |     pub rust_alt: Vec<u8>,
[INFO] [stdout]     |         ^^^^^^^^
[INFO] [stdout] 460 |     pub java_alt: Vec<u8>,
[INFO] [stdout]     |         ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `PathBasesHoldoutRow` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `first_m`, `mismatches`, and `cap` are never read
[INFO] [stdout]    --> gatk-haplotypecaller/src/../tests/dangling_recovery/assembly_dangling_recovery_tests.rs:197:5
[INFO] [stdout]     |
[INFO] [stdout] 194 | struct SixR34EncodingDecision {
[INFO] [stdout]     |        ---------------------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 197 |     first_m: usize,
[INFO] [stdout]     |     ^^^^^^^
[INFO] [stdout] 198 |     mismatches: usize,
[INFO] [stdout]     |     ^^^^^^^^^^
[INFO] [stdout] 199 |     mismatch_positions: Vec<usize>,
[INFO] [stdout] 200 |     cap: usize,
[INFO] [stdout]     |     ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type alias `Java44MakeBlockError` is never used
[INFO] [stdout]  --> gatk-haplotypecaller/src/../tests/event_map/event_map_java44.rs:9:10
[INFO] [stdout]   |
[INFO] [stdout] 9 | pub type Java44MakeBlockError = MakeBlockError;
[INFO] [stdout]   |          ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `unclassified_hint` is never read
[INFO] [stdout]   --> gatk-haplotypecaller/src/hc_profile/mod.rs:55:5
[INFO] [stdout]    |
[INFO] [stdout] 46 | struct ProfileState {
[INFO] [stdout]    |        ------------ field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 55 |     unclassified_hint: bool,
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `hap_oriented_denom` is never read
[INFO] [stdout]    --> gatk-haplotypecaller/src/hc_profile/pairhmm.rs:119:9
[INFO] [stdout]     |
[INFO] [stdout] 112 | pub struct PairHmmOccupancy {
[INFO] [stdout]     |            ---------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 119 |     pub hap_oriented_denom: u64,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `PairHmmOccupancy` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `logless_build_transitions` is never used
[INFO] [stdout]    --> gatk-haplotypecaller/src/pairhmm_logless.rs:131:15
[INFO] [stdout]     |
[INFO] [stdout] 131 | pub(crate) fn logless_build_transitions(
[INFO] [stdout]     |               ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `REF_CORE` is never used
[INFO] [stdout]   --> gatk-haplotypecaller/src/seq_graph_p12_k85_topology_test.rs:21:11
[INFO] [stdout]    |
[INFO] [stdout] 21 |     const REF_CORE: &[u8] = b"TTCATG";
[INFO] [stdout]    |           ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `ALT_WIN` is never used
[INFO] [stdout]   --> gatk-haplotypecaller/src/seq_graph_p12_k85_threading_test.rs:19:11
[INFO] [stdout]    |
[INFO] [stdout] 19 |     const ALT_WIN: &[u8] = b"CTTTTATGTGATGTAT";
[INFO] [stdout]    |           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: constant `REF_WIN` is never used
[INFO] [stdout]   --> gatk-haplotypecaller/src/seq_graph_p12_k85_threading_test.rs:20:11
[INFO] [stdout]    |
[INFO] [stdout] 20 |     const REF_WIN: &[u8] = b"CTTTTTCATGATGTAT";
[INFO] [stdout]    |           ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `raw_qd`, `gaussian`, and `stream_gaussians_after` are never read
[INFO] [stdout]    --> gatk-haplotypecaller/src/annotator/plugins/qual_by_depth.rs:230:9
[INFO] [stdout]     |
[INFO] [stdout] 228 | pub struct QdDrawTrace {
[INFO] [stdout]     |            ----------- fields in this struct
[INFO] [stdout] 229 |     pub site: Option<(String, u64)>,
[INFO] [stdout] 230 |     pub raw_qd: f64,
[INFO] [stdout]     |         ^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 233 |     pub gaussian: Option<f64>,
[INFO] [stdout]     |         ^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 236 |     pub stream_gaussians_after: u64,
[INFO] [stdout]     |         ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `QdDrawTrace` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 30s
[INFO] running `Command { std: "docker" "inspect" "71091c4cd2996605775d846153874ec5a01532704f561b088dac8bedc7d04fc8", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "71091c4cd2996605775d846153874ec5a01532704f561b088dac8bedc7d04fc8", kill_on_drop: false }`
[INFO] [stdout] 71091c4cd2996605775d846153874ec5a01532704f561b088dac8bedc7d04fc8
