[INFO] cloning repository https://github.com/bluenote-1577/haplotype_phaser
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/bluenote-1577/haplotype_phaser" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fhaplotype_phaser", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fhaplotype_phaser'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] e3f281875173515a17b85611fc74a1ae598c120d
[INFO] building bluenote-1577/haplotype_phaser against try#d79d87d4c0f7f0d0785ad6e493cf8cf718ed89a6 for pr-146237-1
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Fhaplotype_phaser" "/workspace/builds/worker-6-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/bluenote-1577/haplotype_phaser
[INFO] finished tweaking git repo https://github.com/bluenote-1577/haplotype_phaser
[INFO] tweaked toml for git repo https://github.com/bluenote-1577/haplotype_phaser written to /workspace/builds/worker-6-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/bluenote-1577/haplotype_phaser on toolchain d79d87d4c0f7f0d0785ad6e493cf8cf718ed89a6
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+d79d87d4c0f7f0d0785ad6e493cf8cf718ed89a6" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/bluenote-1577/haplotype_phaser already has a lockfile, it will not be regenerated
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+d79d87d4c0f7f0d0785ad6e493cf8cf718ed89a6" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] [stdout] bfcd625365e529afe47f4ce0f958a4a3641f8b8b0dedf15639d5fdcf12be3127
[INFO] running `Command { std: "docker" "start" "-a" "bfcd625365e529afe47f4ce0f958a4a3641f8b8b0dedf15639d5fdcf12be3127", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "bfcd625365e529afe47f4ce0f958a4a3641f8b8b0dedf15639d5fdcf12be3127", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "bfcd625365e529afe47f4ce0f958a4a3641f8b8b0dedf15639d5fdcf12be3127", kill_on_drop: false }`
[INFO] [stdout] bfcd625365e529afe47f4ce0f958a4a3641f8b8b0dedf15639d5fdcf12be3127
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+d79d87d4c0f7f0d0785ad6e493cf8cf718ed89a6" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 5481d1b15107f5c9abf350ff5bb7022d99f00f6096d3e0ef4644203ff3f821e3
[INFO] running `Command { std: "docker" "start" "-a" "5481d1b15107f5c9abf350ff5bb7022d99f00f6096d3e0ef4644203ff3f821e3", kill_on_drop: false }`
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[INFO] [stderr]    Compiling memchr v2.3.3
[INFO] [stderr]    Compiling standback v0.2.9
[INFO] [stderr]    Compiling pkg-config v0.3.18
[INFO] [stderr]    Compiling typenum v1.12.0
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[INFO] [stderr]    Compiling jobserver v0.1.21
[INFO] [stderr]    Compiling cc v1.0.59
[INFO] [stderr]    Compiling memoffset v0.5.5
[INFO] [stderr]    Compiling crossbeam-epoch v0.8.2
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[INFO] [stderr]    Compiling time-macros v0.1.0
[INFO] [stderr]    Compiling nalgebra v0.19.0
[INFO] [stderr]    Compiling bio-types v0.7.0
[INFO] [stderr]    Compiling atty v0.2.14
[INFO] [stderr]    Compiling either v1.6.0
[INFO] [stderr]    Compiling vec_map v0.8.2
[INFO] [stderr]    Compiling custom_derive v0.1.7
[INFO] [stderr]    Compiling ansi_term v0.11.0
[INFO] [stderr]    Compiling linear-map v1.2.0
[INFO] [stderr]    Compiling ieee754 v0.2.6
[INFO] [stderr]    Compiling strsim v0.8.0
[INFO] [stderr]    Compiling clap v2.33.3
[INFO] [stderr]    Compiling fxhash v0.2.1
[INFO] [stderr]    Compiling rand_pcg v0.2.1
[INFO] [stderr]    Compiling permute v0.1.0
[INFO] [stderr]    Compiling statrs v0.13.0
[INFO] [stderr]    Compiling rust-htslib v0.32.0
[INFO] [stderr]    Compiling flopp v0.2.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused macro definition: `debug`
[INFO] [stdout]   --> src/local_clustering.rs:11:14
[INFO] [stdout]    |
[INFO] [stdout] 11 | macro_rules! debug {
[INFO] [stdout]    |              ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_macros)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `block`
[INFO] [stdout]    --> src/file_reader.rs:134:13
[INFO] [stdout]     |
[INFO] [stdout] 134 |     for (i, block) in blocks.iter().enumerate() {
[INFO] [stdout]     |             ^^^^^ help: if this is intentional, prefix it with an underscore: `_block`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `number_references` is assigned to, but never used
[INFO] [stdout]    --> src/file_reader.rs:262:13
[INFO] [stdout]     |
[INFO] [stdout] 262 |     let mut number_references = 0;
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_number_references` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `number_references` is never read
[INFO] [stdout]    --> src/file_reader.rs:265:13
[INFO] [stdout]     |
[INFO] [stdout] 265 |             number_references = content.len();
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `dist`
[INFO] [stdout]    --> src/vcf_polishing.rs:717:17
[INFO] [stdout]     |
[INFO] [stdout] 717 |             let dist = &part_size_distribution_sum[j];
[INFO] [stdout]     |                 ^^^^ help: if this is intentional, prefix it with an underscore: `_dist`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `all_frags`
[INFO] [stdout]    --> src/vcf_polishing.rs:641:5
[INFO] [stdout]     |
[INFO] [stdout] 641 |     all_frags: &'a Vec<Frag>,
[INFO] [stdout]     |     ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_all_frags`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `populate_clusters2_binom` is never used
[INFO] [stdout]    --> src/local_clustering.rs:427:4
[INFO] [stdout]     |
[INFO] [stdout] 427 | fn populate_clusters2_binom(
[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 `populate_clusters1` is never used
[INFO] [stdout]    --> src/local_clustering.rs:525:4
[INFO] [stdout]     |
[INFO] [stdout] 525 | fn populate_clusters1(
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_best_perms_mec` is never used
[INFO] [stdout]    --> src/vcf_polishing.rs:118:4
[INFO] [stdout]     |
[INFO] [stdout] 118 | fn get_best_perms_mec(part1: &Vec<FxHashSet<&Frag>>, part2: &Vec<FxHashSet<&Frag>>) -> Vec<Vec<usize>> {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_mec_from_part` is never used
[INFO] [stdout]    --> src/vcf_polishing.rs:249:4
[INFO] [stdout]     |
[INFO] [stdout] 249 | fn get_mec_from_part(part : &Vec<FxHashSet<&Frag>>) -> i32{
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: using `.clone()` on a double reference, which returns `&[u8]` instead of cloning the inner type
[INFO] [stdout]    --> src/file_reader.rs:365:30
[INFO] [stdout]     |
[INFO] [stdout] 365 |         keys.insert(ref_chrom.clone());
[INFO] [stdout]     |                              ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(suspicious_double_ref_op)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [optimized + debuginfo] target(s) in 3m 58s
[INFO] running `Command { std: "docker" "inspect" "5481d1b15107f5c9abf350ff5bb7022d99f00f6096d3e0ef4644203ff3f821e3", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "5481d1b15107f5c9abf350ff5bb7022d99f00f6096d3e0ef4644203ff3f821e3", kill_on_drop: false }`
[INFO] [stdout] 5481d1b15107f5c9abf350ff5bb7022d99f00f6096d3e0ef4644203ff3f821e3
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc2/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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+d79d87d4c0f7f0d0785ad6e493cf8cf718ed89a6" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 2f12449e699e4ae98dad8aae0e862aecde006de72efae0ccaf96a678f971f7c2
[INFO] running `Command { std: "docker" "start" "-a" "2f12449e699e4ae98dad8aae0e862aecde006de72efae0ccaf96a678f971f7c2", kill_on_drop: false }`
[INFO] [stderr]    Compiling doc-comment v0.3.3
[INFO] [stderr]    Compiling predicates-core v1.0.0
[INFO] [stderr]    Compiling float-cmp v0.8.0
[INFO] [stderr]    Compiling treeline v0.1.0
[INFO] [stderr]    Compiling difference v2.0.0
[INFO] [stderr]    Compiling normalize-line-endings v0.3.0
[INFO] [stderr]    Compiling wait-timeout v0.2.0
[INFO] [stdout] warning: unused macro definition: `debug`
[INFO] [stdout]   --> src/local_clustering.rs:11:14
[INFO] [stdout]    |
[INFO] [stdout] 11 | macro_rules! debug {
[INFO] [stdout]    |              ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_macros)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `block`
[INFO] [stdout]    --> src/file_reader.rs:134:13
[INFO] [stdout]     |
[INFO] [stdout] 134 |     for (i, block) in blocks.iter().enumerate() {
[INFO] [stdout]     |             ^^^^^ help: if this is intentional, prefix it with an underscore: `_block`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `number_references` is assigned to, but never used
[INFO] [stdout]    --> src/file_reader.rs:262:13
[INFO] [stdout]     |
[INFO] [stdout] 262 |     let mut number_references = 0;
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_number_references` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `number_references` is never read
[INFO] [stdout]    --> src/file_reader.rs:265:13
[INFO] [stdout]     |
[INFO] [stdout] 265 |             number_references = content.len();
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `dist`
[INFO] [stdout]    --> src/vcf_polishing.rs:717:17
[INFO] [stdout]     |
[INFO] [stdout] 717 |             let dist = &part_size_distribution_sum[j];
[INFO] [stdout]     |                 ^^^^ help: if this is intentional, prefix it with an underscore: `_dist`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `all_frags`
[INFO] [stdout]    --> src/vcf_polishing.rs:641:5
[INFO] [stdout]     |
[INFO] [stdout] 641 |     all_frags: &'a Vec<Frag>,
[INFO] [stdout]     |     ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_all_frags`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `populate_clusters2_binom` is never used
[INFO] [stdout]    --> src/local_clustering.rs:427:4
[INFO] [stdout]     |
[INFO] [stdout] 427 | fn populate_clusters2_binom(
[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 `populate_clusters1` is never used
[INFO] [stdout]    --> src/local_clustering.rs:525:4
[INFO] [stdout]     |
[INFO] [stdout] 525 | fn populate_clusters1(
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_best_perms_mec` is never used
[INFO] [stdout]    --> src/vcf_polishing.rs:118:4
[INFO] [stdout]     |
[INFO] [stdout] 118 | fn get_best_perms_mec(part1: &Vec<FxHashSet<&Frag>>, part2: &Vec<FxHashSet<&Frag>>) -> Vec<Vec<usize>> {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_mec_from_part` is never used
[INFO] [stdout]    --> src/vcf_polishing.rs:249:4
[INFO] [stdout]     |
[INFO] [stdout] 249 | fn get_mec_from_part(part : &Vec<FxHashSet<&Frag>>) -> i32{
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: using `.clone()` on a double reference, which returns `&[u8]` instead of cloning the inner type
[INFO] [stdout]    --> src/file_reader.rs:365:30
[INFO] [stdout]     |
[INFO] [stdout] 365 |         keys.insert(ref_chrom.clone());
[INFO] [stdout]     |                              ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(suspicious_double_ref_op)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]    Compiling predicates-tree v1.0.0
[INFO] [stderr]    Compiling predicates v1.0.5
[INFO] [stderr]    Compiling assert_cmd v1.0.1
[INFO] [stderr]    Compiling flopp v0.2.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `predicates::prelude::*`
[INFO] [stdout]  --> tests/integration_test.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use predicates::prelude::*; // Used for writing assertions
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::time::Instant`
[INFO] [stdout]  --> tests/frag_reader_test.rs:1:5
[INFO] [stdout]   |
[INFO] [stdout] 1 | use std::time::Instant;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `FxHashMap`
[INFO] [stdout]  --> tests/frag_reader_test.rs:5:24
[INFO] [stdout]   |
[INFO] [stdout] 5 | use fxhash::{FxHashSet,FxHashMap};
[INFO] [stdout]   |                        ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `BTreeMap` and `HashSet`
[INFO] [stdout]  --> tests/frag_reader_test.rs:6:24
[INFO] [stdout]   |
[INFO] [stdout] 6 | use std::collections::{HashSet,BTreeMap};
[INFO] [stdout]   |                        ^^^^^^^ ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `indexed_reads`
[INFO] [stdout]   --> tests/frag_reader_test.rs:57:9
[INFO] [stdout]    |
[INFO] [stdout] 57 |     let indexed_reads = utils_frags::get_all_overlaps(frags);
[INFO] [stdout]    |         ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_indexed_reads`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused macro definition: `debug`
[INFO] [stdout]   --> src/local_clustering.rs:11:14
[INFO] [stdout]    |
[INFO] [stdout] 11 | macro_rules! debug {
[INFO] [stdout]    |              ^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_macros)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `block`
[INFO] [stdout]    --> src/file_reader.rs:134:13
[INFO] [stdout]     |
[INFO] [stdout] 134 |     for (i, block) in blocks.iter().enumerate() {
[INFO] [stdout]     |             ^^^^^ help: if this is intentional, prefix it with an underscore: `_block`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `number_references` is assigned to, but never used
[INFO] [stdout]    --> src/file_reader.rs:262:13
[INFO] [stdout]     |
[INFO] [stdout] 262 |     let mut number_references = 0;
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_number_references` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `number_references` is never read
[INFO] [stdout]    --> src/file_reader.rs:265:13
[INFO] [stdout]     |
[INFO] [stdout] 265 |             number_references = content.len();
[INFO] [stdout]     |             ^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `dist`
[INFO] [stdout]    --> src/vcf_polishing.rs:717:17
[INFO] [stdout]     |
[INFO] [stdout] 717 |             let dist = &part_size_distribution_sum[j];
[INFO] [stdout]     |                 ^^^^ help: if this is intentional, prefix it with an underscore: `_dist`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `all_frags`
[INFO] [stdout]    --> src/vcf_polishing.rs:641:5
[INFO] [stdout]     |
[INFO] [stdout] 641 |     all_frags: &'a Vec<Frag>,
[INFO] [stdout]     |     ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_all_frags`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `populate_clusters2_binom` is never used
[INFO] [stdout]    --> src/local_clustering.rs:427:4
[INFO] [stdout]     |
[INFO] [stdout] 427 | fn populate_clusters2_binom(
[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 `populate_clusters1` is never used
[INFO] [stdout]    --> src/local_clustering.rs:525:4
[INFO] [stdout]     |
[INFO] [stdout] 525 | fn populate_clusters1(
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_best_perms_mec` is never used
[INFO] [stdout]    --> src/vcf_polishing.rs:118:4
[INFO] [stdout]     |
[INFO] [stdout] 118 | fn get_best_perms_mec(part1: &Vec<FxHashSet<&Frag>>, part2: &Vec<FxHashSet<&Frag>>) -> Vec<Vec<usize>> {
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_mec_from_part` is never used
[INFO] [stdout]    --> src/vcf_polishing.rs:249:4
[INFO] [stdout]     |
[INFO] [stdout] 249 | fn get_mec_from_part(part : &Vec<FxHashSet<&Frag>>) -> i32{
[INFO] [stdout]     |    ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: using `.clone()` on a double reference, which returns `&[u8]` instead of cloning the inner type
[INFO] [stdout]    --> src/file_reader.rs:365:30
[INFO] [stdout]     |
[INFO] [stdout] 365 |         keys.insert(ref_chrom.clone());
[INFO] [stdout]     |                              ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(suspicious_double_ref_op)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `test` profile [optimized + debuginfo] target(s) in 11.48s
[INFO] running `Command { std: "docker" "inspect" "2f12449e699e4ae98dad8aae0e862aecde006de72efae0ccaf96a678f971f7c2", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "2f12449e699e4ae98dad8aae0e862aecde006de72efae0ccaf96a678f971f7c2", kill_on_drop: false }`
[INFO] [stdout] 2f12449e699e4ae98dad8aae0e862aecde006de72efae0ccaf96a678f971f7c2
