[INFO] fetching crate longcallR 1.12.0...
[INFO] building longcallR-1.12.0 against master#c7f6aa2869acdbf014d094c6e427e554e160b6db for pr-146237-2
[INFO] extracting crate longcallR 1.12.0 into /workspace/builds/worker-5-tc1/source
[INFO] started tweaking crates.io crate longcallR 1.12.0
[INFO] finished tweaking crates.io crate longcallR 1.12.0
[INFO] tweaked toml for crates.io crate longcallR 1.12.0 written to /workspace/builds/worker-5-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate longcallR 1.12.0 on toolchain c7f6aa2869acdbf014d094c6e427e554e160b6db
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate longcallR 1.12.0 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" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 61f909482ac7154aad1d96275f80e9492cba30b3c220913d6a59f3182a2d2697
[INFO] running `Command { std: "docker" "start" "-a" "61f909482ac7154aad1d96275f80e9492cba30b3c220913d6a59f3182a2d2697", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "61f909482ac7154aad1d96275f80e9492cba30b3c220913d6a59f3182a2d2697", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "61f909482ac7154aad1d96275f80e9492cba30b3c220913d6a59f3182a2d2697", kill_on_drop: false }`
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[INFO] [stdout] 19baca08002c6c67296cca153b681cda9e2e08862fc035d2a86365d882a3a361
[INFO] running `Command { std: "docker" "start" "-a" "19baca08002c6c67296cca153b681cda9e2e08862fc035d2a86365d882a3a361", kill_on_drop: false }`
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[INFO] [stderr]    Compiling longcallR v1.12.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `min`
[INFO] [stdout]  --> src/candidate.rs:2:16
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::cmp::{min, Ordering};
[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: `HashSet`
[INFO] [stdout]  --> src/candidate.rs:3:33
[INFO] [stdout]   |
[INFO] [stdout] 3 | use std::collections::{HashMap, HashSet};
[INFO] [stdout]   |                                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Platform`
[INFO] [stdout]   --> src/candidate.rs:13:13
[INFO] [stdout]    |
[INFO] [stdout] 13 | use crate::{Platform, VALID_ALLELES};
[INFO] [stdout]    |             ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::exon::Exon`
[INFO] [stdout]  --> src/fragment.rs:1:5
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::exon::Exon;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::hash::Hash`
[INFO] [stdout]  --> src/snp.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::hash::Hash;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `probability::distribution::Distribution`
[INFO] [stdout]  --> src/snp.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use probability::distribution::Distribution;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::exon::Exon`
[INFO] [stdout]  --> src/snp.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use crate::exon::Exon;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `LD_Pair` should have an upper camel case name
[INFO] [stdout]   --> src/snp.rs:93:12
[INFO] [stdout]    |
[INFO] [stdout] 93 | pub struct LD_Pair {
[INFO] [stdout]    |            ^^^^^^^ help: convert the identifier to upper camel case: `LdPair`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(non_camel_case_types)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> src/phase.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `logprob` is never read
[INFO] [stdout]    --> src/candidate.rs:238:21
[INFO] [stdout]     |
[INFO] [stdout] 238 |             let mut logprob = [0.0, 0.0, 0.0];
[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: variable does not need to be mutable
[INFO] [stdout]    --> src/candidate.rs:241:17
[INFO] [stdout]     |
[INFO] [stdout] 241 |             let mut identical_baseqs;
[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]    --> src/candidate.rs:242:17
[INFO] [stdout]     |
[INFO] [stdout] 242 |             let mut different_baseqs;
[INFO] [stdout]     |                 ----^^^^^^^^^^^^^^^^
[INFO] [stdout]     |                 |
[INFO] [stdout]     |                 help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/candidate.rs:324:17
[INFO] [stdout]     |
[INFO] [stdout] 324 |             let mut genotype_prob = [
[INFO] [stdout]     |                 ----^^^^^^^^^^^^^
[INFO] [stdout]     |                 |
[INFO] [stdout]     |                 help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp1_ref_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:638:26
[INFO] [stdout]     |
[INFO] [stdout] 638 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                          ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp1_alt_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:638:45
[INFO] [stdout]     |
[INFO] [stdout] 638 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                                             ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp2_ref_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:638:64
[INFO] [stdout]     |
[INFO] [stdout] 638 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                                                                ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp2_alt_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:638:83
[INFO] [stdout]     |
[INFO] [stdout] 638 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                                                                                   ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/candidate.rs:637:22
[INFO] [stdout]     |
[INFO] [stdout] 637 |                 let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt);
[INFO] [stdout]     |                      ----^^^^^^^^
[INFO] [stdout]     |                      |
[INFO] [stdout]     |                      help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/candidate.rs:637:36
[INFO] [stdout]     |
[INFO] [stdout] 637 |                 let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt);
[INFO] [stdout]     |                                    ----^^^^^^^^
[INFO] [stdout]     |                                    |
[INFO] [stdout]     |                                    help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/candidate.rs:637:50
[INFO] [stdout]     |
[INFO] [stdout] 637 |                 let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt);
[INFO] [stdout]     |                                                  ----^^^^^^^^
[INFO] [stdout]     |                                                  |
[INFO] [stdout]     |                                                  help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/candidate.rs:637:64
[INFO] [stdout]     |
[INFO] [stdout] 637 |                 let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt);
[INFO] [stdout]     |                                                                ----^^^^^^^^
[INFO] [stdout]     |                                                                |
[INFO] [stdout]     |                                                                help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp_pos` is never read
[INFO] [stdout]   --> src/fragment.rs:61:21
[INFO] [stdout]    |
[INFO] [stdout] 61 |             let mut snp_pos = -1; // pre-computed position of candidate SNPs
[INFO] [stdout]    |                     ^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `ref_base`
[INFO] [stdout]    --> src/fragment.rs:101:33
[INFO] [stdout]     |
[INFO] [stdout] 101 | ...                   let ref_base = ref_seq[pos_on_ref as usize] as char;
[INFO] [stdout]     |                           ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_base`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `read_base`
[INFO] [stdout]    --> src/fragment.rs:102:33
[INFO] [stdout]     |
[INFO] [stdout] 102 | ...                   let read_base = seq[pos_on_query as usize] as char;
[INFO] [stdout]     |                           ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_base`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `read_baseq`
[INFO] [stdout]    --> src/fragment.rs:103:33
[INFO] [stdout]     |
[INFO] [stdout] 103 | ...                   let read_baseq = record.qual()[pos_on_query as usize];
[INFO] [stdout]     |                           ^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout] help: if this is intentional, prefix it with an underscore
[INFO] [stdout]     |
[INFO] [stdout] 103 |                             let _read_baseq = record.qual()[pos_on_query as usize];
[INFO] [stdout]     |                                 +
[INFO] [stdout] help: you might have meant to pattern match on the similarly named constant `MAX_BASE_QUALITY`
[INFO] [stdout]     |
[INFO] [stdout] 103 -                             let read_baseq = record.qual()[pos_on_query as usize];
[INFO] [stdout] 103 +                             let constants::MAX_BASE_QUALITY = record.qual()[pos_on_query as usize];
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/fragment.rs:210:25
[INFO] [stdout]     |
[INFO] [stdout] 210 |                     let mut pair_start_idx: usize;
[INFO] [stdout]     |                         ----^^^^^^^^^^^^^^
[INFO] [stdout]     |                         |
[INFO] [stdout]     |                         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/fragment.rs:211:25
[INFO] [stdout]     |
[INFO] [stdout] 211 |                     let mut pair_end_idx: usize;
[INFO] [stdout]     |                         ----^^^^^^^^^^^^
[INFO] [stdout]     |                         |
[INFO] [stdout]     |                         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/fragment.rs:212:25
[INFO] [stdout]     |
[INFO] [stdout] 212 |                     let mut pair_start_base: u8;
[INFO] [stdout]     |                         ----^^^^^^^^^^^^^^^
[INFO] [stdout]     |                         |
[INFO] [stdout]     |                         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/fragment.rs:213:25
[INFO] [stdout]     |
[INFO] [stdout] 213 |                     let mut pair_end_base: u8;
[INFO] [stdout]     |                         ----^^^^^^^^^^^^^
[INFO] [stdout]     |                         |
[INFO] [stdout]     |                         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/fragment.rs:318:25
[INFO] [stdout]     |
[INFO] [stdout] 318 |                     let mut frag = &mut self.fragments[frag_idx];
[INFO] [stdout]     |                         ----^^^^
[INFO] [stdout]     |                         |
[INFO] [stdout]     |                         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/phase.rs:15:9
[INFO] [stdout]    |
[INFO] [stdout] 15 |     let mut x: i32;
[INFO] [stdout]    |         ----^
[INFO] [stdout]    |         |
[INFO] [stdout]    |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/phase.rs:38:9
[INFO] [stdout]    |
[INFO] [stdout] 38 |     let mut x: i32;
[INFO] [stdout]    |         ----^
[INFO] [stdout]    |         |
[INFO] [stdout]    |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `weight` is never read
[INFO] [stdout]    --> src/phase.rs:638:29
[INFO] [stdout]     |
[INFO] [stdout] 638 |                     let mut weight = 0;
[INFO] [stdout]     |                             ^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `haplotype_genotype_increase` is never read
[INFO] [stdout]    --> src/phase.rs:867:17
[INFO] [stdout]     |
[INFO] [stdout] 867 |                 haplotype_genotype_increase = true;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `max_q` is never read
[INFO] [stdout]    --> src/phase.rs:923:29
[INFO] [stdout]     |
[INFO] [stdout] 923 |                     let mut max_q = 0.0;
[INFO] [stdout]     |                             ^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `q1` is never read
[INFO] [stdout]     --> src/phase.rs:1039:26
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                          ^^
[INFO] [stdout]      |
[INFO] [stdout]      = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `q2` is never read
[INFO] [stdout]     --> src/phase.rs:1039:34
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                                  ^^
[INFO] [stdout]      |
[INFO] [stdout]      = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `q3`
[INFO] [stdout]     --> src/phase.rs:1039:42
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                                          ^^ help: if this is intentional, prefix it with an underscore: `_q3`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `q4`
[INFO] [stdout]     --> src/phase.rs:1039:50
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                                                  ^^ help: if this is intentional, prefix it with an underscore: `_q4`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]     --> src/phase.rs:1039:38
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                                      ----^^
[INFO] [stdout]      |                                      |
[INFO] [stdout]      |                                      help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]     --> src/phase.rs:1039:46
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                                              ----^^
[INFO] [stdout]      |                                              |
[INFO] [stdout]      |                                              help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `pA` is never read
[INFO] [stdout]    --> src/snp.rs:111:18
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                  ^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `pa` is assigned to, but never used
[INFO] [stdout]    --> src/snp.rs:111:26
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                          ^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_pa` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `pB` is never read
[INFO] [stdout]    --> src/snp.rs:111:34
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                                  ^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `pb` is assigned to, but never used
[INFO] [stdout]    --> src/snp.rs:111:42
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                                          ^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_pb` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `pa` is never read
[INFO] [stdout]    --> src/snp.rs:141:9
[INFO] [stdout]     |
[INFO] [stdout] 141 |         pa = aB + ab; // P(a)
[INFO] [stdout]     |         ^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `pb` is never read
[INFO] [stdout]    --> src/snp.rs:143:9
[INFO] [stdout]     |
[INFO] [stdout] 143 |         pb = Ab + ab; // P(b)
[INFO] [stdout]     |         ^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/snp.rs:145:13
[INFO] [stdout]     |
[INFO] [stdout] 145 |         let mut d = AB - pA * pB; // D= P(AB) - P(A)P(B)
[INFO] [stdout]     |             ----^
[INFO] [stdout]     |             |
[INFO] [stdout]     |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp_pos` is never read
[INFO] [stdout]   --> src/snpfrags.rs:86:21
[INFO] [stdout]    |
[INFO] [stdout] 86 |             let mut snp_pos = -1; // pre-computed position of candidate SNPs
[INFO] [stdout]    |                     ^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `alleles` is assigned to, but never used
[INFO] [stdout]   --> src/snpfrags.rs:87:21
[INFO] [stdout]    |
[INFO] [stdout] 87 |             let mut alleles; // pre-computed alleles of candidate SNPs
[INFO] [stdout]    |                     ^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_alleles` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]   --> src/snpfrags.rs:90:17
[INFO] [stdout]    |
[INFO] [stdout] 90 |                 alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stdout]    |                 ^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:104:17
[INFO] [stdout]     |
[INFO] [stdout] 104 |                 alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stdout]     |                 ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:141:37
[INFO] [stdout]     |
[INFO] [stdout] 141 | ...                   alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:157:37
[INFO] [stdout]     |
[INFO] [stdout] 157 | ...                   alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:169:37
[INFO] [stdout]     |
[INFO] [stdout] 169 | ...                   alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score1` is never read
[INFO] [stdout]    --> src/snpfrags.rs:237:21
[INFO] [stdout]     |
[INFO] [stdout] 237 |             let mut phase_score1 = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score2` is never read
[INFO] [stdout]    --> src/snpfrags.rs:238:21
[INFO] [stdout]     |
[INFO] [stdout] 238 |             let mut phase_score2 = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score` is never read
[INFO] [stdout]    --> src/snpfrags.rs:239:21
[INFO] [stdout]     |
[INFO] [stdout] 239 |             let mut phase_score = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score1` is never read
[INFO] [stdout]    --> src/snpfrags.rs:329:21
[INFO] [stdout]     |
[INFO] [stdout] 329 |             let mut phase_score1 = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score2` is never read
[INFO] [stdout]    --> src/snpfrags.rs:330:21
[INFO] [stdout]     |
[INFO] [stdout] 330 |             let mut phase_score2 = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score` is never read
[INFO] [stdout]    --> src/snpfrags.rs:331:21
[INFO] [stdout]     |
[INFO] [stdout] 331 |             let mut phase_score = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `eta_i`
[INFO] [stdout]    --> src/snpfrags.rs:396:17
[INFO] [stdout]     |
[INFO] [stdout] 396 |             let eta_i = snp.genotype;
[INFO] [stdout]     |                 ^^^^^ help: if this is intentional, prefix it with an underscore: `_eta_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score` is never read
[INFO] [stdout]    --> src/snpfrags.rs:480:21
[INFO] [stdout]     |
[INFO] [stdout] 480 |             let mut phase_score = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `q` is never read
[INFO] [stdout]    --> src/snpfrags.rs:577:25
[INFO] [stdout]     |
[INFO] [stdout] 577 |                 let mut q = 0.0;
[INFO] [stdout]     |                         ^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `qn` is never read
[INFO] [stdout]    --> src/snpfrags.rs:578:25
[INFO] [stdout]     |
[INFO] [stdout] 578 |                 let mut qn = 0.0;
[INFO] [stdout]     |                         ^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `region`
[INFO] [stdout]    --> src/snpfrags.rs:708:13
[INFO] [stdout]     |
[INFO] [stdout] 708 |         let region = self.region.clone().to_string();
[INFO] [stdout]     |             ^^^^^^ help: if this is intentional, prefix it with an underscore: `_region`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]  --> src/somatic.rs:6:9
[INFO] [stdout]   |
[INFO] [stdout] 6 |     let mut hap1_allele_class;
[INFO] [stdout]   |         ----^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |         |
[INFO] [stdout]   |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]  --> src/somatic.rs:7:9
[INFO] [stdout]   |
[INFO] [stdout] 7 |     let mut hap2_allele_class;
[INFO] [stdout]   |         ----^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |         |
[INFO] [stdout]   |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `cgi`
[INFO] [stdout]    --> src/util.rs:699:29
[INFO] [stdout]     |
[INFO] [stdout] 699 |                         for cgi in 0..cg.len() {
[INFO] [stdout]     |                             ^^^ help: if this is intentional, prefix it with an underscore: `_cgi`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `gt` is never read
[INFO] [stdout]   --> src/vcf.rs:54:25
[INFO] [stdout]    |
[INFO] [stdout] 54 |                 let mut gt = "0/0";
[INFO] [stdout]    |                         ^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `Exon` is never constructed
[INFO] [stdout]  --> src/exon.rs:4:12
[INFO] [stdout]   |
[INFO] [stdout] 4 | pub struct Exon {
[INFO] [stdout]   |            ^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `clean_fragments` is never used
[INFO] [stdout]    --> src/fragment.rs:311:12
[INFO] [stdout]     |
[INFO] [stdout]   9 | impl SNPFrag {
[INFO] [stdout]     | ------------ method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 311 |     pub fn clean_fragments(&mut self) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `qki` is never used
[INFO] [stdout]   --> src/phase.rs:14:8
[INFO] [stdout]    |
[INFO] [stdout] 14 | pub fn qki(sigma: i32, delta: i32, alt_fraction: f32, base_allele: i32, error_rate: f64) -> f64 {
[INFO] [stdout]    |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `cal_sigma_delta` is never used
[INFO] [stdout]   --> src/phase.rs:51:8
[INFO] [stdout]    |
[INFO] [stdout] 51 | pub fn cal_sigma_delta(sigma_k: i32, delta: &Vec<i32>, altfrac: &Vec<f32>, ps: &Vec<i32>, probs: &Vec<f64>) -> f64 {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `cal_delta_sigma` is never used
[INFO] [stdout]   --> src/phase.rs:98:8
[INFO] [stdout]    |
[INFO] [stdout] 98 | pub fn cal_delta_sigma(delta_i: i32, alt_fraction_i: f32, sigma: &Vec<i32>, ps: &Vec<i32>, probs: &Vec<f64>) -> f64 {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `check_block_new_haplotype_haplotag` is never used
[INFO] [stdout]    --> src/phase.rs:357:8
[INFO] [stdout]     |
[INFO] [stdout] 357 | pub fn check_block_new_haplotype_haplotag(snpfrag: &SNPFrag, updated_haplotype: &HashMap<usize, i32>, updated_haplotag: &HashMap<usize, i...
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `cal_inconsistent_percentage` is never used
[INFO] [stdout]    --> src/phase.rs:401:8
[INFO] [stdout]     |
[INFO] [stdout] 401 | pub fn cal_inconsistent_percentage(delta_i: i32, sigma: &Vec<i32>, ps: &Vec<i32>) -> f64 {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_blocks` is never used
[INFO] [stdout]    --> src/phase.rs:411:8
[INFO] [stdout]     |
[INFO] [stdout] 411 | pub fn get_blocks(block_links: &HashMap<[usize; 2], i32>, weight_threshold: u32) -> (Vec<Vec<usize>>, GraphMap<usize, i32, Undirected>) {
[INFO] [stdout]     |        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `hap1_ref_baseqs`, `hap1_alt_baseqs`, `hap2_ref_baseqs`, and `hap2_alt_baseqs` are never read
[INFO] [stdout]   --> src/snp.rs:10:9
[INFO] [stdout]    |
[INFO] [stdout]  9 | pub struct HapQuals {
[INFO] [stdout]    |            -------- fields in this struct
[INFO] [stdout] 10 |     pub hap1_ref_baseqs: Vec<u8>,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^
[INFO] [stdout] 11 |     pub hap1_alt_baseqs: Vec<u8>,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^
[INFO] [stdout] 12 |     pub hap2_ref_baseqs: Vec<u8>,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^
[INFO] [stdout] 13 |     pub hap2_alt_baseqs: Vec<u8>,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `HapQuals` 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: struct `AlleleClass` is never constructed
[INFO] [stdout]   --> src/snp.rs:17:12
[INFO] [stdout]    |
[INFO] [stdout] 17 | pub struct AlleleClass {
[INFO] [stdout]    |            ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `somatic`, `somatic_score`, and `hap_quals` are never read
[INFO] [stdout]   --> src/snp.rs:82:9
[INFO] [stdout]    |
[INFO] [stdout] 40 | pub struct CandidateSNP {
[INFO] [stdout]    |            ------------ fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 82 |     pub somatic: bool,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 83 |     // detected somatic mutation by model
[INFO] [stdout] 84 |     pub somatic_score: f64,
[INFO] [stdout]    |         ^^^^^^^^^^^^^
[INFO] [stdout] 85 |     // phred somatic score
[INFO] [stdout] 86 |     pub hap_quals: HapQuals,
[INFO] [stdout]    |         ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `CandidateSNP` 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: method `calculate_LD_R2` is never used
[INFO] [stdout]    --> src/snp.rs:107:12
[INFO] [stdout]     |
[INFO] [stdout] 106 | impl LD_Pair {
[INFO] [stdout]     | ------------ method in this implementation
[INFO] [stdout] 107 |     pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `block_id` is never read
[INFO] [stdout]    --> src/snp.rs:243:9
[INFO] [stdout]     |
[INFO] [stdout] 242 | pub struct Block {
[INFO] [stdout]     |            ----- field in this struct
[INFO] [stdout] 243 |     pub block_id: u32,
[INFO] [stdout]     |         ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `Block` 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: field `phased` is never read
[INFO] [stdout]   --> src/snpfrags.rs:29:9
[INFO] [stdout]    |
[INFO] [stdout] 15 | pub struct SNPFrag {
[INFO] [stdout]    |            ------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 29 |     pub phased: bool,
[INFO] [stdout]    |         ^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `SNPFrag` 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: methods `get_somatic_haplotype_baseqs` and `detect_somatic_by_het` are never used
[INFO] [stdout]    --> src/snpfrags.rs:56:12
[INFO] [stdout]     |
[INFO] [stdout]  55 | impl SNPFrag {
[INFO] [stdout]     | ------------ methods in this implementation
[INFO] [stdout]  56 |     pub fn get_somatic_haplotype_baseqs(&mut self, bam_path: &str, region: &Region, phased_fragments: &HashMap<String, i32>) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 735 |     pub fn detect_somatic_by_het(&mut self, bam_path: &str, region: &Region) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `calculate_prob_somatic` is never used
[INFO] [stdout]  --> src/somatic.rs:5:8
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub fn calculate_prob_somatic(hap1_ref_baseqs: &Vec<u8>, hap1_alt_baseqs: &Vec<u8>, hap2_ref_baseqs: &Vec<u8>, hap2_alt_baseqs: &Vec<u8>,...
[INFO] [stdout]   |        ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `get_main_alleles` and `get_none_ref_count` are never used
[INFO] [stdout]    --> src/util.rs:178:12
[INFO] [stdout]     |
[INFO] [stdout] 129 | impl BaseFreq {
[INFO] [stdout]     | ------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 178 |     pub fn get_main_alleles(&self) -> Vec<(char, u32)> {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 203 |     pub fn get_none_ref_count(&self) -> u32 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `load_vcf` is never used
[INFO] [stdout]    --> src/vcf.rs:309:8
[INFO] [stdout]     |
[INFO] [stdout] 309 | pub fn load_vcf(
[INFO] [stdout]     |        ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `phased` is never read
[INFO] [stdout]    --> src/vcf.rs:397:9
[INFO] [stdout]     |
[INFO] [stdout] 394 | pub struct GenotypeAndQuality {
[INFO] [stdout]     |            ------------------ field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 397 |     pub phased: bool,
[INFO] [stdout]     |         ^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `GenotypeAndQuality` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `init_haplotypes_LD2` should have a snake case name
[INFO] [stdout]    --> src/phase.rs:609:19
[INFO] [stdout]     |
[INFO] [stdout] 609 |     pub unsafe fn init_haplotypes_LD2(&mut self, ld_graph: &GraphMap<usize, i32, Undirected>, ld_weight_threshold: u32) -> HashSet<usize> {
[INFO] [stdout]     |                   ^^^^^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `init_haplotypes_ld2`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `calculate_LD_R2` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:107:12
[INFO] [stdout]     |
[INFO] [stdout] 107 |     pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `calculate_ld_r2`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `A` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:107:35
[INFO] [stdout]     |
[INFO] [stdout] 107 |     pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 {
[INFO] [stdout]     |                                   ^ help: convert the identifier to snake case: `a`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `B` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:107:49
[INFO] [stdout]     |
[INFO] [stdout] 107 |     pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 {
[INFO] [stdout]     |                                                 ^ help: convert the identifier to snake case: `b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `AB` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:110:18
[INFO] [stdout]     |
[INFO] [stdout] 110 |         let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                  ^^ help: convert the identifier to snake case: `ab`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `Ab` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:110:26
[INFO] [stdout]     |
[INFO] [stdout] 110 |         let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                          ^^ help: convert the identifier to snake case: `ab`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `aB` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:110:34
[INFO] [stdout]     |
[INFO] [stdout] 110 |         let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                                  ^^ help: convert the identifier to snake case: `a_b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `pA` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:111:18
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                  ^^ help: convert the identifier to snake case: `p_a`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `pB` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:111:34
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                                  ^^ help: convert the identifier to snake case: `p_b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `A` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:158:32
[INFO] [stdout]     |
[INFO] [stdout] 158 |     pub fn calculate_ld(&self, A: u8, a: u8, B: u8, b: u8) -> (f32, i32) {
[INFO] [stdout]     |                                ^ help: convert the identifier to snake case: `a`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `B` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:158:46
[INFO] [stdout]     |
[INFO] [stdout] 158 |     pub fn calculate_ld(&self, A: u8, a: u8, B: u8, b: u8) -> (f32, i32) {
[INFO] [stdout]     |                                              ^ help: convert the identifier to snake case: `b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 07s
[INFO] running `Command { std: "docker" "inspect" "19baca08002c6c67296cca153b681cda9e2e08862fc035d2a86365d882a3a361", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "19baca08002c6c67296cca153b681cda9e2e08862fc035d2a86365d882a3a361", kill_on_drop: false }`
[INFO] [stdout] 19baca08002c6c67296cca153b681cda9e2e08862fc035d2a86365d882a3a361
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-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:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 53ff017707b88bf68ebfdfd07dbacdd657f0e2a721587b8d96b19a24c06e5ef2
[INFO] running `Command { std: "docker" "start" "-a" "53ff017707b88bf68ebfdfd07dbacdd657f0e2a721587b8d96b19a24c06e5ef2", kill_on_drop: false }`
[INFO] [stderr]    Compiling longcallR v1.12.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `min`
[INFO] [stdout]  --> src/candidate.rs:2:16
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::cmp::{min, Ordering};
[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: `HashSet`
[INFO] [stdout]  --> src/candidate.rs:3:33
[INFO] [stdout]   |
[INFO] [stdout] 3 | use std::collections::{HashMap, HashSet};
[INFO] [stdout]   |                                 ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `Platform`
[INFO] [stdout]   --> src/candidate.rs:13:13
[INFO] [stdout]    |
[INFO] [stdout] 13 | use crate::{Platform, VALID_ALLELES};
[INFO] [stdout]    |             ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::exon::Exon`
[INFO] [stdout]  --> src/fragment.rs:1:5
[INFO] [stdout]   |
[INFO] [stdout] 1 | use crate::exon::Exon;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::hash::Hash`
[INFO] [stdout]  --> src/snp.rs:2:5
[INFO] [stdout]   |
[INFO] [stdout] 2 | use std::hash::Hash;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `probability::distribution::Distribution`
[INFO] [stdout]  --> src/snp.rs:4:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | use probability::distribution::Distribution;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `crate::exon::Exon`
[INFO] [stdout]  --> src/snp.rs:6:5
[INFO] [stdout]   |
[INFO] [stdout] 6 | use crate::exon::Exon;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: type `LD_Pair` should have an upper camel case name
[INFO] [stdout]   --> src/snp.rs:93:12
[INFO] [stdout]    |
[INFO] [stdout] 93 | pub struct LD_Pair {
[INFO] [stdout]    |            ^^^^^^^ help: convert the identifier to upper camel case: `LdPair`
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(non_camel_case_types)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `itertools::Itertools`
[INFO] [stdout]  --> src/phase.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use itertools::Itertools;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `logprob` is never read
[INFO] [stdout]    --> src/candidate.rs:238:21
[INFO] [stdout]     |
[INFO] [stdout] 238 |             let mut logprob = [0.0, 0.0, 0.0];
[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: variable does not need to be mutable
[INFO] [stdout]    --> src/candidate.rs:241:17
[INFO] [stdout]     |
[INFO] [stdout] 241 |             let mut identical_baseqs;
[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]    --> src/candidate.rs:242:17
[INFO] [stdout]     |
[INFO] [stdout] 242 |             let mut different_baseqs;
[INFO] [stdout]     |                 ----^^^^^^^^^^^^^^^^
[INFO] [stdout]     |                 |
[INFO] [stdout]     |                 help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/candidate.rs:324:17
[INFO] [stdout]     |
[INFO] [stdout] 324 |             let mut genotype_prob = [
[INFO] [stdout]     |                 ----^^^^^^^^^^^^^
[INFO] [stdout]     |                 |
[INFO] [stdout]     |                 help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp1_ref_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:638:26
[INFO] [stdout]     |
[INFO] [stdout] 638 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                          ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp1_alt_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:638:45
[INFO] [stdout]     |
[INFO] [stdout] 638 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                                             ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp2_ref_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:638:64
[INFO] [stdout]     |
[INFO] [stdout] 638 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                                                                ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp2_alt_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:638:83
[INFO] [stdout]     |
[INFO] [stdout] 638 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                                                                                   ^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/candidate.rs:637:22
[INFO] [stdout]     |
[INFO] [stdout] 637 |                 let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt);
[INFO] [stdout]     |                      ----^^^^^^^^
[INFO] [stdout]     |                      |
[INFO] [stdout]     |                      help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/candidate.rs:637:36
[INFO] [stdout]     |
[INFO] [stdout] 637 |                 let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt);
[INFO] [stdout]     |                                    ----^^^^^^^^
[INFO] [stdout]     |                                    |
[INFO] [stdout]     |                                    help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/candidate.rs:637:50
[INFO] [stdout]     |
[INFO] [stdout] 637 |                 let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt);
[INFO] [stdout]     |                                                  ----^^^^^^^^
[INFO] [stdout]     |                                                  |
[INFO] [stdout]     |                                                  help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/candidate.rs:637:64
[INFO] [stdout]     |
[INFO] [stdout] 637 |                 let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt);
[INFO] [stdout]     |                                                                ----^^^^^^^^
[INFO] [stdout]     |                                                                |
[INFO] [stdout]     |                                                                help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp_pos` is never read
[INFO] [stdout]   --> src/fragment.rs:61:21
[INFO] [stdout]    |
[INFO] [stdout] 61 |             let mut snp_pos = -1; // pre-computed position of candidate SNPs
[INFO] [stdout]    |                     ^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `ref_base`
[INFO] [stdout]    --> src/fragment.rs:101:33
[INFO] [stdout]     |
[INFO] [stdout] 101 | ...                   let ref_base = ref_seq[pos_on_ref as usize] as char;
[INFO] [stdout]     |                           ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_base`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `read_base`
[INFO] [stdout]    --> src/fragment.rs:102:33
[INFO] [stdout]     |
[INFO] [stdout] 102 | ...                   let read_base = seq[pos_on_query as usize] as char;
[INFO] [stdout]     |                           ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_base`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `read_baseq`
[INFO] [stdout]    --> src/fragment.rs:103:33
[INFO] [stdout]     |
[INFO] [stdout] 103 | ...                   let read_baseq = record.qual()[pos_on_query as usize];
[INFO] [stdout]     |                           ^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout] help: if this is intentional, prefix it with an underscore
[INFO] [stdout]     |
[INFO] [stdout] 103 |                             let _read_baseq = record.qual()[pos_on_query as usize];
[INFO] [stdout]     |                                 +
[INFO] [stdout] help: you might have meant to pattern match on the similarly named constant `MAX_BASE_QUALITY`
[INFO] [stdout]     |
[INFO] [stdout] 103 -                             let read_baseq = record.qual()[pos_on_query as usize];
[INFO] [stdout] 103 +                             let constants::MAX_BASE_QUALITY = record.qual()[pos_on_query as usize];
[INFO] [stdout]     |
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/fragment.rs:210:25
[INFO] [stdout]     |
[INFO] [stdout] 210 |                     let mut pair_start_idx: usize;
[INFO] [stdout]     |                         ----^^^^^^^^^^^^^^
[INFO] [stdout]     |                         |
[INFO] [stdout]     |                         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/fragment.rs:211:25
[INFO] [stdout]     |
[INFO] [stdout] 211 |                     let mut pair_end_idx: usize;
[INFO] [stdout]     |                         ----^^^^^^^^^^^^
[INFO] [stdout]     |                         |
[INFO] [stdout]     |                         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/fragment.rs:212:25
[INFO] [stdout]     |
[INFO] [stdout] 212 |                     let mut pair_start_base: u8;
[INFO] [stdout]     |                         ----^^^^^^^^^^^^^^^
[INFO] [stdout]     |                         |
[INFO] [stdout]     |                         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/fragment.rs:213:25
[INFO] [stdout]     |
[INFO] [stdout] 213 |                     let mut pair_end_base: u8;
[INFO] [stdout]     |                         ----^^^^^^^^^^^^^
[INFO] [stdout]     |                         |
[INFO] [stdout]     |                         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/fragment.rs:318:25
[INFO] [stdout]     |
[INFO] [stdout] 318 |                     let mut frag = &mut self.fragments[frag_idx];
[INFO] [stdout]     |                         ----^^^^
[INFO] [stdout]     |                         |
[INFO] [stdout]     |                         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/phase.rs:15:9
[INFO] [stdout]    |
[INFO] [stdout] 15 |     let mut x: i32;
[INFO] [stdout]    |         ----^
[INFO] [stdout]    |         |
[INFO] [stdout]    |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]   --> src/phase.rs:38:9
[INFO] [stdout]    |
[INFO] [stdout] 38 |     let mut x: i32;
[INFO] [stdout]    |         ----^
[INFO] [stdout]    |         |
[INFO] [stdout]    |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `weight` is never read
[INFO] [stdout]    --> src/phase.rs:638:29
[INFO] [stdout]     |
[INFO] [stdout] 638 |                     let mut weight = 0;
[INFO] [stdout]     |                             ^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `haplotype_genotype_increase` is never read
[INFO] [stdout]    --> src/phase.rs:867:17
[INFO] [stdout]     |
[INFO] [stdout] 867 |                 haplotype_genotype_increase = true;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `max_q` is never read
[INFO] [stdout]    --> src/phase.rs:923:29
[INFO] [stdout]     |
[INFO] [stdout] 923 |                     let mut max_q = 0.0;
[INFO] [stdout]     |                             ^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `q1` is never read
[INFO] [stdout]     --> src/phase.rs:1039:26
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                          ^^
[INFO] [stdout]      |
[INFO] [stdout]      = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `q2` is never read
[INFO] [stdout]     --> src/phase.rs:1039:34
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                                  ^^
[INFO] [stdout]      |
[INFO] [stdout]      = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `q3`
[INFO] [stdout]     --> src/phase.rs:1039:42
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                                          ^^ help: if this is intentional, prefix it with an underscore: `_q3`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `q4`
[INFO] [stdout]     --> src/phase.rs:1039:50
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                                                  ^^ help: if this is intentional, prefix it with an underscore: `_q4`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]     --> src/phase.rs:1039:38
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                                      ----^^
[INFO] [stdout]      |                                      |
[INFO] [stdout]      |                                      help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]     --> src/phase.rs:1039:46
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                                              ----^^
[INFO] [stdout]      |                                              |
[INFO] [stdout]      |                                              help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `pA` is never read
[INFO] [stdout]    --> src/snp.rs:111:18
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                  ^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `pa` is assigned to, but never used
[INFO] [stdout]    --> src/snp.rs:111:26
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                          ^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_pa` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `pB` is never read
[INFO] [stdout]    --> src/snp.rs:111:34
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                                  ^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `pb` is assigned to, but never used
[INFO] [stdout]    --> src/snp.rs:111:42
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                                          ^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_pb` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `pa` is never read
[INFO] [stdout]    --> src/snp.rs:141:9
[INFO] [stdout]     |
[INFO] [stdout] 141 |         pa = aB + ab; // P(a)
[INFO] [stdout]     |         ^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `pb` is never read
[INFO] [stdout]    --> src/snp.rs:143:9
[INFO] [stdout]     |
[INFO] [stdout] 143 |         pb = Ab + ab; // P(b)
[INFO] [stdout]     |         ^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/snp.rs:145:13
[INFO] [stdout]     |
[INFO] [stdout] 145 |         let mut d = AB - pA * pB; // D= P(AB) - P(A)P(B)
[INFO] [stdout]     |             ----^
[INFO] [stdout]     |             |
[INFO] [stdout]     |             help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp_pos` is never read
[INFO] [stdout]   --> src/snpfrags.rs:86:21
[INFO] [stdout]    |
[INFO] [stdout] 86 |             let mut snp_pos = -1; // pre-computed position of candidate SNPs
[INFO] [stdout]    |                     ^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `alleles` is assigned to, but never used
[INFO] [stdout]   --> src/snpfrags.rs:87:21
[INFO] [stdout]    |
[INFO] [stdout] 87 |             let mut alleles; // pre-computed alleles of candidate SNPs
[INFO] [stdout]    |                     ^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: consider using `_alleles` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]   --> src/snpfrags.rs:90:17
[INFO] [stdout]    |
[INFO] [stdout] 90 |                 alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stdout]    |                 ^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:104:17
[INFO] [stdout]     |
[INFO] [stdout] 104 |                 alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stdout]     |                 ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:141:37
[INFO] [stdout]     |
[INFO] [stdout] 141 | ...                   alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:157:37
[INFO] [stdout]     |
[INFO] [stdout] 157 | ...                   alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:169:37
[INFO] [stdout]     |
[INFO] [stdout] 169 | ...                   alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score1` is never read
[INFO] [stdout]    --> src/snpfrags.rs:237:21
[INFO] [stdout]     |
[INFO] [stdout] 237 |             let mut phase_score1 = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score2` is never read
[INFO] [stdout]    --> src/snpfrags.rs:238:21
[INFO] [stdout]     |
[INFO] [stdout] 238 |             let mut phase_score2 = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score` is never read
[INFO] [stdout]    --> src/snpfrags.rs:239:21
[INFO] [stdout]     |
[INFO] [stdout] 239 |             let mut phase_score = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score1` is never read
[INFO] [stdout]    --> src/snpfrags.rs:329:21
[INFO] [stdout]     |
[INFO] [stdout] 329 |             let mut phase_score1 = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score2` is never read
[INFO] [stdout]    --> src/snpfrags.rs:330:21
[INFO] [stdout]     |
[INFO] [stdout] 330 |             let mut phase_score2 = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score` is never read
[INFO] [stdout]    --> src/snpfrags.rs:331:21
[INFO] [stdout]     |
[INFO] [stdout] 331 |             let mut phase_score = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `eta_i`
[INFO] [stdout]    --> src/snpfrags.rs:396:17
[INFO] [stdout]     |
[INFO] [stdout] 396 |             let eta_i = snp.genotype;
[INFO] [stdout]     |                 ^^^^^ help: if this is intentional, prefix it with an underscore: `_eta_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score` is never read
[INFO] [stdout]    --> src/snpfrags.rs:480:21
[INFO] [stdout]     |
[INFO] [stdout] 480 |             let mut phase_score = 0.0;
[INFO] [stdout]     |                     ^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `q` is never read
[INFO] [stdout]    --> src/snpfrags.rs:577:25
[INFO] [stdout]     |
[INFO] [stdout] 577 |                 let mut q = 0.0;
[INFO] [stdout]     |                         ^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `qn` is never read
[INFO] [stdout]    --> src/snpfrags.rs:578:25
[INFO] [stdout]     |
[INFO] [stdout] 578 |                 let mut qn = 0.0;
[INFO] [stdout]     |                         ^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `region`
[INFO] [stdout]    --> src/snpfrags.rs:708:13
[INFO] [stdout]     |
[INFO] [stdout] 708 |         let region = self.region.clone().to_string();
[INFO] [stdout]     |             ^^^^^^ help: if this is intentional, prefix it with an underscore: `_region`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]  --> src/somatic.rs:6:9
[INFO] [stdout]   |
[INFO] [stdout] 6 |     let mut hap1_allele_class;
[INFO] [stdout]   |         ----^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |         |
[INFO] [stdout]   |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]  --> src/somatic.rs:7:9
[INFO] [stdout]   |
[INFO] [stdout] 7 |     let mut hap2_allele_class;
[INFO] [stdout]   |         ----^^^^^^^^^^^^^^^^^
[INFO] [stdout]   |         |
[INFO] [stdout]   |         help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `cgi`
[INFO] [stdout]    --> src/util.rs:699:29
[INFO] [stdout]     |
[INFO] [stdout] 699 |                         for cgi in 0..cg.len() {
[INFO] [stdout]     |                             ^^^ help: if this is intentional, prefix it with an underscore: `_cgi`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `gt` is never read
[INFO] [stdout]   --> src/vcf.rs:54:25
[INFO] [stdout]    |
[INFO] [stdout] 54 |                 let mut gt = "0/0";
[INFO] [stdout]    |                         ^^
[INFO] [stdout]    |
[INFO] [stdout]    = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `Exon` is never constructed
[INFO] [stdout]  --> src/exon.rs:4:12
[INFO] [stdout]   |
[INFO] [stdout] 4 | pub struct Exon {
[INFO] [stdout]   |            ^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `clean_fragments` is never used
[INFO] [stdout]    --> src/fragment.rs:311:12
[INFO] [stdout]     |
[INFO] [stdout]   9 | impl SNPFrag {
[INFO] [stdout]     | ------------ method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 311 |     pub fn clean_fragments(&mut self) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `qki` is never used
[INFO] [stdout]   --> src/phase.rs:14:8
[INFO] [stdout]    |
[INFO] [stdout] 14 | pub fn qki(sigma: i32, delta: i32, alt_fraction: f32, base_allele: i32, error_rate: f64) -> f64 {
[INFO] [stdout]    |        ^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `cal_sigma_delta` is never used
[INFO] [stdout]   --> src/phase.rs:51:8
[INFO] [stdout]    |
[INFO] [stdout] 51 | pub fn cal_sigma_delta(sigma_k: i32, delta: &Vec<i32>, altfrac: &Vec<f32>, ps: &Vec<i32>, probs: &Vec<f64>) -> f64 {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `cal_delta_sigma` is never used
[INFO] [stdout]   --> src/phase.rs:98:8
[INFO] [stdout]    |
[INFO] [stdout] 98 | pub fn cal_delta_sigma(delta_i: i32, alt_fraction_i: f32, sigma: &Vec<i32>, ps: &Vec<i32>, probs: &Vec<f64>) -> f64 {
[INFO] [stdout]    |        ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `check_block_new_haplotype_haplotag` is never used
[INFO] [stdout]    --> src/phase.rs:357:8
[INFO] [stdout]     |
[INFO] [stdout] 357 | pub fn check_block_new_haplotype_haplotag(snpfrag: &SNPFrag, updated_haplotype: &HashMap<usize, i32>, updated_haplotag: &HashMap<usize, i...
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `cal_inconsistent_percentage` is never used
[INFO] [stdout]    --> src/phase.rs:401:8
[INFO] [stdout]     |
[INFO] [stdout] 401 | pub fn cal_inconsistent_percentage(delta_i: i32, sigma: &Vec<i32>, ps: &Vec<i32>) -> f64 {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `get_blocks` is never used
[INFO] [stdout]    --> src/phase.rs:411:8
[INFO] [stdout]     |
[INFO] [stdout] 411 | pub fn get_blocks(block_links: &HashMap<[usize; 2], i32>, weight_threshold: u32) -> (Vec<Vec<usize>>, GraphMap<usize, i32, Undirected>) {
[INFO] [stdout]     |        ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `hap1_ref_baseqs`, `hap1_alt_baseqs`, `hap2_ref_baseqs`, and `hap2_alt_baseqs` are never read
[INFO] [stdout]   --> src/snp.rs:10:9
[INFO] [stdout]    |
[INFO] [stdout]  9 | pub struct HapQuals {
[INFO] [stdout]    |            -------- fields in this struct
[INFO] [stdout] 10 |     pub hap1_ref_baseqs: Vec<u8>,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^
[INFO] [stdout] 11 |     pub hap1_alt_baseqs: Vec<u8>,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^
[INFO] [stdout] 12 |     pub hap2_ref_baseqs: Vec<u8>,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^
[INFO] [stdout] 13 |     pub hap2_alt_baseqs: Vec<u8>,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `HapQuals` 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: struct `AlleleClass` is never constructed
[INFO] [stdout]   --> src/snp.rs:17:12
[INFO] [stdout]    |
[INFO] [stdout] 17 | pub struct AlleleClass {
[INFO] [stdout]    |            ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `somatic`, `somatic_score`, and `hap_quals` are never read
[INFO] [stdout]   --> src/snp.rs:82:9
[INFO] [stdout]    |
[INFO] [stdout] 40 | pub struct CandidateSNP {
[INFO] [stdout]    |            ------------ fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 82 |     pub somatic: bool,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout] 83 |     // detected somatic mutation by model
[INFO] [stdout] 84 |     pub somatic_score: f64,
[INFO] [stdout]    |         ^^^^^^^^^^^^^
[INFO] [stdout] 85 |     // phred somatic score
[INFO] [stdout] 86 |     pub hap_quals: HapQuals,
[INFO] [stdout]    |         ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `CandidateSNP` 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: method `calculate_LD_R2` is never used
[INFO] [stdout]    --> src/snp.rs:107:12
[INFO] [stdout]     |
[INFO] [stdout] 106 | impl LD_Pair {
[INFO] [stdout]     | ------------ method in this implementation
[INFO] [stdout] 107 |     pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `block_id` is never read
[INFO] [stdout]    --> src/snp.rs:243:9
[INFO] [stdout]     |
[INFO] [stdout] 242 | pub struct Block {
[INFO] [stdout]     |            ----- field in this struct
[INFO] [stdout] 243 |     pub block_id: u32,
[INFO] [stdout]     |         ^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `Block` 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: field `phased` is never read
[INFO] [stdout]   --> src/snpfrags.rs:29:9
[INFO] [stdout]    |
[INFO] [stdout] 15 | pub struct SNPFrag {
[INFO] [stdout]    |            ------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 29 |     pub phased: bool,
[INFO] [stdout]    |         ^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `SNPFrag` 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: methods `get_somatic_haplotype_baseqs` and `detect_somatic_by_het` are never used
[INFO] [stdout]    --> src/snpfrags.rs:56:12
[INFO] [stdout]     |
[INFO] [stdout]  55 | impl SNPFrag {
[INFO] [stdout]     | ------------ methods in this implementation
[INFO] [stdout]  56 |     pub fn get_somatic_haplotype_baseqs(&mut self, bam_path: &str, region: &Region, phased_fragments: &HashMap<String, i32>) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 735 |     pub fn detect_somatic_by_het(&mut self, bam_path: &str, region: &Region) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `calculate_prob_somatic` is never used
[INFO] [stdout]  --> src/somatic.rs:5:8
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub fn calculate_prob_somatic(hap1_ref_baseqs: &Vec<u8>, hap1_alt_baseqs: &Vec<u8>, hap2_ref_baseqs: &Vec<u8>, hap2_alt_baseqs: &Vec<u8>,...
[INFO] [stdout]   |        ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `get_main_alleles` and `get_none_ref_count` are never used
[INFO] [stdout]    --> src/util.rs:178:12
[INFO] [stdout]     |
[INFO] [stdout] 129 | impl BaseFreq {
[INFO] [stdout]     | ------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 178 |     pub fn get_main_alleles(&self) -> Vec<(char, u32)> {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 203 |     pub fn get_none_ref_count(&self) -> u32 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `load_vcf` is never used
[INFO] [stdout]    --> src/vcf.rs:309:8
[INFO] [stdout]     |
[INFO] [stdout] 309 | pub fn load_vcf(
[INFO] [stdout]     |        ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `phased` is never read
[INFO] [stdout]    --> src/vcf.rs:397:9
[INFO] [stdout]     |
[INFO] [stdout] 394 | pub struct GenotypeAndQuality {
[INFO] [stdout]     |            ------------------ field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 397 |     pub phased: bool,
[INFO] [stdout]     |         ^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `GenotypeAndQuality` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `init_haplotypes_LD2` should have a snake case name
[INFO] [stdout]    --> src/phase.rs:609:19
[INFO] [stdout]     |
[INFO] [stdout] 609 |     pub unsafe fn init_haplotypes_LD2(&mut self, ld_graph: &GraphMap<usize, i32, Undirected>, ld_weight_threshold: u32) -> HashSet<usize> {
[INFO] [stdout]     |                   ^^^^^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `init_haplotypes_ld2`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `calculate_LD_R2` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:107:12
[INFO] [stdout]     |
[INFO] [stdout] 107 |     pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `calculate_ld_r2`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `A` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:107:35
[INFO] [stdout]     |
[INFO] [stdout] 107 |     pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 {
[INFO] [stdout]     |                                   ^ help: convert the identifier to snake case: `a`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `B` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:107:49
[INFO] [stdout]     |
[INFO] [stdout] 107 |     pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 {
[INFO] [stdout]     |                                                 ^ help: convert the identifier to snake case: `b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `AB` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:110:18
[INFO] [stdout]     |
[INFO] [stdout] 110 |         let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                  ^^ help: convert the identifier to snake case: `ab`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `Ab` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:110:26
[INFO] [stdout]     |
[INFO] [stdout] 110 |         let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                          ^^ help: convert the identifier to snake case: `ab`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `aB` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:110:34
[INFO] [stdout]     |
[INFO] [stdout] 110 |         let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                                  ^^ help: convert the identifier to snake case: `a_b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `pA` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:111:18
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                  ^^ help: convert the identifier to snake case: `p_a`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `pB` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:111:34
[INFO] [stdout]     |
[INFO] [stdout] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                                  ^^ help: convert the identifier to snake case: `p_b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `A` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:158:32
[INFO] [stdout]     |
[INFO] [stdout] 158 |     pub fn calculate_ld(&self, A: u8, a: u8, B: u8, b: u8) -> (f32, i32) {
[INFO] [stdout]     |                                ^ help: convert the identifier to snake case: `a`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `B` should have a snake case name
[INFO] [stdout]    --> src/snp.rs:158:46
[INFO] [stdout]     |
[INFO] [stdout] 158 |     pub fn calculate_ld(&self, A: u8, a: u8, B: u8, b: u8) -> (f32, i32) {
[INFO] [stdout]     |                                              ^ help: convert the identifier to snake case: `b`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 1.83s
[INFO] running `Command { std: "docker" "inspect" "53ff017707b88bf68ebfdfd07dbacdd657f0e2a721587b8d96b19a24c06e5ef2", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "53ff017707b88bf68ebfdfd07dbacdd657f0e2a721587b8d96b19a24c06e5ef2", kill_on_drop: false }`
[INFO] [stdout] 53ff017707b88bf68ebfdfd07dbacdd657f0e2a721587b8d96b19a24c06e5ef2
