[INFO] fetching crate longcallR 1.12.0...
[INFO] testing longcallR-1.12.0 against master#2fd6efc32704647e64d3d646d21c4c68eae100e4 for pr-149852-1
[INFO] extracting crate longcallR 1.12.0 into /workspace/builds/worker-6-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-6-tc1/source/Cargo.toml
[INFO] validating manifest of crates.io crate longcallR 1.12.0 on toolchain 2fd6efc32704647e64d3d646d21c4c68eae100e4
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+2fd6efc32704647e64d3d646d21c4c68eae100e4" "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" "+2fd6efc32704647e64d3d646d21c4c68eae100e4" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:aa71247004a7fa38d13ec170f48f06cdedf5bc50b2a8645e56ed7e992e6fa513" "/opt/rustwide/cargo-home/bin/cargo" "+2fd6efc32704647e64d3d646d21c4c68eae100e4" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 017f87c9458b1b5c57398446151d5702050906a3717c209aa28da234515f5f96
[INFO] running `Command { std: "docker" "start" "-a" "017f87c9458b1b5c57398446151d5702050906a3717c209aa28da234515f5f96", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "017f87c9458b1b5c57398446151d5702050906a3717c209aa28da234515f5f96", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "start" "-a" "3fe865f44af23602c43c4877f94676cc5deb42939ee5dcaad571c1587b9529cf", kill_on_drop: false }`
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[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: 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 `logprob` is never read
[INFO] [stdout]    --> src/candidate.rs:238:31
[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: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 `snp1_ref_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:638:22
[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:638:41
[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:638:60
[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:638:79
[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/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: 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]     |                           ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_baseq`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp_pos` is never read
[INFO] [stdout]   --> src/fragment.rs:61:31
[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: 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:638:38
[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:923:37
[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: 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: unused variable: `q3`
[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]      |                                      ^^^^^^ 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:1039:46
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                                              ^^^^^^ help: if this is intentional, prefix it with an underscore: `_q4`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `q1` is never read
[INFO] [stdout]     --> src/phase.rs:1039:22
[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:1039:30
[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: 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: variable `pa` is assigned to, but never used
[INFO] [stdout]    --> src/snp.rs:111:22
[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: variable `pb` is assigned to, but never used
[INFO] [stdout]    --> src/snp.rs:111:38
[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:111:14
[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: 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:111:30
[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: 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 `alleles` is assigned to, but never used
[INFO] [stdout]   --> src/snpfrags.rs:87:17
[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 `snp_pos` is never read
[INFO] [stdout]   --> src/snpfrags.rs:86:31
[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: 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: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: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:237:36
[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:238:36
[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:239:35
[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:329:36
[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:330:36
[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:331:35
[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:480:35
[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:577:29
[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:578:30
[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:54:30
[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<us...
[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, Undirect...
[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<...
[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<...
[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 06s
[INFO] running `Command { std: "docker" "inspect" "3fe865f44af23602c43c4877f94676cc5deb42939ee5dcaad571c1587b9529cf", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "3fe865f44af23602c43c4877f94676cc5deb42939ee5dcaad571c1587b9529cf", kill_on_drop: false }`
[INFO] [stdout] 3fe865f44af23602c43c4877f94676cc5deb42939ee5dcaad571c1587b9529cf
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:aa71247004a7fa38d13ec170f48f06cdedf5bc50b2a8645e56ed7e992e6fa513" "/opt/rustwide/cargo-home/bin/cargo" "+2fd6efc32704647e64d3d646d21c4c68eae100e4" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 06473c42e78f198a3866ec5409149004875d894000e5df49b01ac9b7ca8cba6f
[INFO] running `Command { std: "docker" "start" "-a" "06473c42e78f198a3866ec5409149004875d894000e5df49b01ac9b7ca8cba6f", 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: 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 `logprob` is never read
[INFO] [stdout]    --> src/candidate.rs:238:31
[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: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 `snp1_ref_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:638:22
[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:638:41
[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:638:60
[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:638:79
[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/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: 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]     |                           ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_baseq`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp_pos` is never read
[INFO] [stdout]   --> src/fragment.rs:61:31
[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: 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:638:38
[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:923:37
[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: 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: unused variable: `q3`
[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]      |                                      ^^^^^^ 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:1039:46
[INFO] [stdout]      |
[INFO] [stdout] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                                              ^^^^^^ help: if this is intentional, prefix it with an underscore: `_q4`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `q1` is never read
[INFO] [stdout]     --> src/phase.rs:1039:22
[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:1039:30
[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: 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: variable `pa` is assigned to, but never used
[INFO] [stdout]    --> src/snp.rs:111:22
[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: variable `pb` is assigned to, but never used
[INFO] [stdout]    --> src/snp.rs:111:38
[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:111:14
[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: 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:111:30
[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: 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 `alleles` is assigned to, but never used
[INFO] [stdout]   --> src/snpfrags.rs:87:17
[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 `snp_pos` is never read
[INFO] [stdout]   --> src/snpfrags.rs:86:31
[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: 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: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: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:237:36
[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:238:36
[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:239:35
[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:329:36
[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:330:36
[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:331:35
[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:480:35
[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:577:29
[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:578:30
[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:54:30
[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<us...
[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, Undirect...
[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<...
[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<...
[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 1.44s
[INFO] running `Command { std: "docker" "inspect" "06473c42e78f198a3866ec5409149004875d894000e5df49b01ac9b7ca8cba6f", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "06473c42e78f198a3866ec5409149004875d894000e5df49b01ac9b7ca8cba6f", kill_on_drop: false }`
[INFO] [stdout] 06473c42e78f198a3866ec5409149004875d894000e5df49b01ac9b7ca8cba6f
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-6-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:aa71247004a7fa38d13ec170f48f06cdedf5bc50b2a8645e56ed7e992e6fa513" "/opt/rustwide/cargo-home/bin/cargo" "+2fd6efc32704647e64d3d646d21c4c68eae100e4" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] 89daf6632f9ae8095642b7ce60d9e66d07a6f366fd37927ea22ddc54c5e79ca2
[INFO] running `Command { std: "docker" "start" "-a" "89daf6632f9ae8095642b7ce60d9e66d07a6f366fd37927ea22ddc54c5e79ca2", kill_on_drop: false }`
[INFO] [stderr] warning: unused import: `min`
[INFO] [stderr]  --> src/candidate.rs:2:16
[INFO] [stderr]   |
[INFO] [stderr] 2 | use std::cmp::{min, Ordering};
[INFO] [stderr]   |                ^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `HashSet`
[INFO] [stderr]  --> src/candidate.rs:3:33
[INFO] [stderr]   |
[INFO] [stderr] 3 | use std::collections::{HashMap, HashSet};
[INFO] [stderr]   |                                 ^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `Platform`
[INFO] [stderr]   --> src/candidate.rs:13:13
[INFO] [stderr]    |
[INFO] [stderr] 13 | use crate::{Platform, VALID_ALLELES};
[INFO] [stderr]    |             ^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `crate::exon::Exon`
[INFO] [stderr]  --> src/fragment.rs:1:5
[INFO] [stderr]   |
[INFO] [stderr] 1 | use crate::exon::Exon;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::hash::Hash`
[INFO] [stderr]  --> src/snp.rs:2:5
[INFO] [stderr]   |
[INFO] [stderr] 2 | use std::hash::Hash;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `probability::distribution::Distribution`
[INFO] [stderr]  --> src/snp.rs:4:5
[INFO] [stderr]   |
[INFO] [stderr] 4 | use probability::distribution::Distribution;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `crate::exon::Exon`
[INFO] [stderr]  --> src/snp.rs:6:5
[INFO] [stderr]   |
[INFO] [stderr] 6 | use crate::exon::Exon;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: type `LD_Pair` should have an upper camel case name
[INFO] [stderr]   --> src/snp.rs:93:12
[INFO] [stderr]    |
[INFO] [stderr] 93 | pub struct LD_Pair {
[INFO] [stderr]    |            ^^^^^^^ help: convert the identifier to upper camel case: `LdPair`
[INFO] [stderr]    |
[INFO] [stderr]    = note: `#[warn(non_camel_case_types)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `itertools::Itertools`
[INFO] [stderr]  --> src/phase.rs:3:5
[INFO] [stderr]   |
[INFO] [stderr] 3 | use itertools::Itertools;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/candidate.rs:241:17
[INFO] [stderr]     |
[INFO] [stderr] 241 |             let mut identical_baseqs;
[INFO] [stderr]     |                 ----^^^^^^^^^^^^^^^^
[INFO] [stderr]     |                 |
[INFO] [stderr]     |                 help: remove this `mut`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/candidate.rs:242:17
[INFO] [stderr]     |
[INFO] [stderr] 242 |             let mut different_baseqs;
[INFO] [stderr]     |                 ----^^^^^^^^^^^^^^^^
[INFO] [stderr]     |                 |
[INFO] [stderr]     |                 help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/candidate.rs:324:17
[INFO] [stderr]     |
[INFO] [stderr] 324 |             let mut genotype_prob = [
[INFO] [stderr]     |                 ----^^^^^^^^^^^^^
[INFO] [stderr]     |                 |
[INFO] [stderr]     |                 help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `logprob` is never read
[INFO] [stderr]    --> src/candidate.rs:238:31
[INFO] [stderr]     |
[INFO] [stderr] 238 |             let mut logprob = [0.0, 0.0, 0.0];
[INFO] [stderr]     |                               ^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/candidate.rs:637:22
[INFO] [stderr]     |
[INFO] [stderr] 637 |                 let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt);
[INFO] [stderr]     |                      ----^^^^^^^^
[INFO] [stderr]     |                      |
[INFO] [stderr]     |                      help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/candidate.rs:637:36
[INFO] [stderr]     |
[INFO] [stderr] 637 |                 let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt);
[INFO] [stderr]     |                                    ----^^^^^^^^
[INFO] [stderr]     |                                    |
[INFO] [stderr]     |                                    help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/candidate.rs:637:50
[INFO] [stderr]     |
[INFO] [stderr] 637 |                 let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt);
[INFO] [stderr]     |                                                  ----^^^^^^^^
[INFO] [stderr]     |                                                  |
[INFO] [stderr]     |                                                  help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/candidate.rs:637:64
[INFO] [stderr]     |
[INFO] [stderr] 637 |                 let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt);
[INFO] [stderr]     |                                                                ----^^^^^^^^
[INFO] [stderr]     |                                                                |
[INFO] [stderr]     |                                                                help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `snp1_ref_frac` is never read
[INFO] [stderr]    --> src/candidate.rs:638:22
[INFO] [stderr]     |
[INFO] [stderr] 638 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stderr]     |                      ^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `snp1_alt_frac` is never read
[INFO] [stderr]    --> src/candidate.rs:638:41
[INFO] [stderr]     |
[INFO] [stderr] 638 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stderr]     |                                         ^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `snp2_ref_frac` is never read
[INFO] [stderr]    --> src/candidate.rs:638:60
[INFO] [stderr]     |
[INFO] [stderr] 638 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stderr]     |                                                            ^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `snp2_alt_frac` is never read
[INFO] [stderr]    --> src/candidate.rs:638:79
[INFO] [stderr]     |
[INFO] [stderr] 638 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stderr]     |                                                                               ^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/fragment.rs:210:25
[INFO] [stderr]     |
[INFO] [stderr] 210 |                     let mut pair_start_idx: usize;
[INFO] [stderr]     |                         ----^^^^^^^^^^^^^^
[INFO] [stderr]     |                         |
[INFO] [stderr]     |                         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/fragment.rs:211:25
[INFO] [stderr]     |
[INFO] [stderr] 211 |                     let mut pair_end_idx: usize;
[INFO] [stderr]     |                         ----^^^^^^^^^^^^
[INFO] [stderr]     |                         |
[INFO] [stderr]     |                         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/fragment.rs:212:25
[INFO] [stderr]     |
[INFO] [stderr] 212 |                     let mut pair_start_base: u8;
[INFO] [stderr]     |                         ----^^^^^^^^^^^^^^^
[INFO] [stderr]     |                         |
[INFO] [stderr]     |                         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/fragment.rs:213:25
[INFO] [stderr]     |
[INFO] [stderr] 213 |                     let mut pair_end_base: u8;
[INFO] [stderr]     |                         ----^^^^^^^^^^^^^
[INFO] [stderr]     |                         |
[INFO] [stderr]     |                         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `ref_base`
[INFO] [stderr]    --> src/fragment.rs:101:33
[INFO] [stderr]     |
[INFO] [stderr] 101 | ...                   let ref_base = ref_seq[pos_on_ref as usize] as char;
[INFO] [stderr]     |                           ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_base`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `read_base`
[INFO] [stderr]    --> src/fragment.rs:102:33
[INFO] [stderr]     |
[INFO] [stderr] 102 | ...                   let read_base = seq[pos_on_query as usize] as char;
[INFO] [stderr]     |                           ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_base`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `read_baseq`
[INFO] [stderr]    --> src/fragment.rs:103:33
[INFO] [stderr]     |
[INFO] [stderr] 103 | ...                   let read_baseq = record.qual()[pos_on_query as usize];
[INFO] [stderr]     |                           ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_baseq`
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `snp_pos` is never read
[INFO] [stderr]   --> src/fragment.rs:61:31
[INFO] [stderr]    |
[INFO] [stderr] 61 |             let mut snp_pos = -1; // pre-computed position of candidate SNPs
[INFO] [stderr]    |                               ^^
[INFO] [stderr]    |
[INFO] [stderr]    = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/fragment.rs:318:25
[INFO] [stderr]     |
[INFO] [stderr] 318 |                     let mut frag = &mut self.fragments[frag_idx];
[INFO] [stderr]     |                         ----^^^^
[INFO] [stderr]     |                         |
[INFO] [stderr]     |                         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]   --> src/phase.rs:15:9
[INFO] [stderr]    |
[INFO] [stderr] 15 |     let mut x: i32;
[INFO] [stderr]    |         ----^
[INFO] [stderr]    |         |
[INFO] [stderr]    |         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]   --> src/phase.rs:38:9
[INFO] [stderr]    |
[INFO] [stderr] 38 |     let mut x: i32;
[INFO] [stderr]    |         ----^
[INFO] [stderr]    |         |
[INFO] [stderr]    |         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `weight` is never read
[INFO] [stderr]    --> src/phase.rs:638:38
[INFO] [stderr]     |
[INFO] [stderr] 638 |                     let mut weight = 0;
[INFO] [stderr]     |                                      ^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `haplotype_genotype_increase` is never read
[INFO] [stderr]    --> src/phase.rs:867:17
[INFO] [stderr]     |
[INFO] [stderr] 867 |                 haplotype_genotype_increase = true;
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `max_q` is never read
[INFO] [stderr]    --> src/phase.rs:923:37
[INFO] [stderr]     |
[INFO] [stderr] 923 |                     let mut max_q = 0.0;
[INFO] [stderr]     |                                     ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]     --> src/phase.rs:1039:38
[INFO] [stderr]      |
[INFO] [stderr] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]      |                                      ----^^
[INFO] [stderr]      |                                      |
[INFO] [stderr]      |                                      help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]     --> src/phase.rs:1039:46
[INFO] [stderr]      |
[INFO] [stderr] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]      |                                              ----^^
[INFO] [stderr]      |                                              |
[INFO] [stderr]      |                                              help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `q3`
[INFO] [stderr]     --> src/phase.rs:1039:38
[INFO] [stderr]      |
[INFO] [stderr] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]      |                                      ^^^^^^ help: if this is intentional, prefix it with an underscore: `_q3`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `q4`
[INFO] [stderr]     --> src/phase.rs:1039:46
[INFO] [stderr]      |
[INFO] [stderr] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]      |                                              ^^^^^^ help: if this is intentional, prefix it with an underscore: `_q4`
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `q1` is never read
[INFO] [stderr]     --> src/phase.rs:1039:22
[INFO] [stderr]      |
[INFO] [stderr] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]      |                      ^^^^^^
[INFO] [stderr]      |
[INFO] [stderr]      = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `q2` is never read
[INFO] [stderr]     --> src/phase.rs:1039:30
[INFO] [stderr]      |
[INFO] [stderr] 1039 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]      |                              ^^^^^^
[INFO] [stderr]      |
[INFO] [stderr]      = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/snp.rs:145:13
[INFO] [stderr]     |
[INFO] [stderr] 145 |         let mut d = AB - pA * pB; // D= P(AB) - P(A)P(B)
[INFO] [stderr]     |             ----^
[INFO] [stderr]     |             |
[INFO] [stderr]     |             help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable `pa` is assigned to, but never used
[INFO] [stderr]    --> src/snp.rs:111:22
[INFO] [stderr]     |
[INFO] [stderr] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]     |                      ^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: consider using `_pa` instead
[INFO] [stderr] 
[INFO] [stderr] warning: variable `pb` is assigned to, but never used
[INFO] [stderr]    --> src/snp.rs:111:38
[INFO] [stderr]     |
[INFO] [stderr] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]     |                                      ^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: consider using `_pb` instead
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `pA` is never read
[INFO] [stderr]    --> src/snp.rs:111:14
[INFO] [stderr]     |
[INFO] [stderr] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]     |              ^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `pa` is never read
[INFO] [stderr]    --> src/snp.rs:141:9
[INFO] [stderr]     |
[INFO] [stderr] 141 |         pa = aB + ab; // P(a)
[INFO] [stderr]     |         ^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `pB` is never read
[INFO] [stderr]    --> src/snp.rs:111:30
[INFO] [stderr]     |
[INFO] [stderr] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]     |                              ^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `pb` is never read
[INFO] [stderr]    --> src/snp.rs:143:9
[INFO] [stderr]     |
[INFO] [stderr] 143 |         pb = Ab + ab; // P(b)
[INFO] [stderr]     |         ^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: variable `alleles` is assigned to, but never used
[INFO] [stderr]   --> src/snpfrags.rs:87:17
[INFO] [stderr]    |
[INFO] [stderr] 87 |             let mut alleles; // pre-computed alleles of candidate SNPs
[INFO] [stderr]    |                 ^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: consider using `_alleles` instead
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `snp_pos` is never read
[INFO] [stderr]   --> src/snpfrags.rs:86:31
[INFO] [stderr]    |
[INFO] [stderr] 86 |             let mut snp_pos = -1; // pre-computed position of candidate SNPs
[INFO] [stderr]    |                               ^^
[INFO] [stderr]    |
[INFO] [stderr]    = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `alleles` is never read
[INFO] [stderr]    --> src/snpfrags.rs:104:17
[INFO] [stderr]     |
[INFO] [stderr] 104 |                 alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `alleles` is never read
[INFO] [stderr]   --> src/snpfrags.rs:90:17
[INFO] [stderr]    |
[INFO] [stderr] 90 |                 alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stderr]    |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `alleles` is never read
[INFO] [stderr]    --> src/snpfrags.rs:141:37
[INFO] [stderr]     |
[INFO] [stderr] 141 | ...                   alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stderr]     |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `alleles` is never read
[INFO] [stderr]    --> src/snpfrags.rs:157:37
[INFO] [stderr]     |
[INFO] [stderr] 157 | ...                   alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stderr]     |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `alleles` is never read
[INFO] [stderr]    --> src/snpfrags.rs:169:37
[INFO] [stderr]     |
[INFO] [stderr] 169 | ...                   alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone();
[INFO] [stderr]     |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `phase_score1` is never read
[INFO] [stderr]    --> src/snpfrags.rs:237:36
[INFO] [stderr]     |
[INFO] [stderr] 237 |             let mut phase_score1 = 0.0;
[INFO] [stderr]     |                                    ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `phase_score2` is never read
[INFO] [stderr]    --> src/snpfrags.rs:238:36
[INFO] [stderr]     |
[INFO] [stderr] 238 |             let mut phase_score2 = 0.0;
[INFO] [stderr]     |                                    ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `phase_score` is never read
[INFO] [stderr]    --> src/snpfrags.rs:239:35
[INFO] [stderr]     |
[INFO] [stderr] 239 |             let mut phase_score = 0.0;
[INFO] [stderr]     |                                   ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `phase_score1` is never read
[INFO] [stderr]    --> src/snpfrags.rs:329:36
[INFO] [stderr]     |
[INFO] [stderr] 329 |             let mut phase_score1 = 0.0;
[INFO] [stderr]     |                                    ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `phase_score2` is never read
[INFO] [stderr]    --> src/snpfrags.rs:330:36
[INFO] [stderr]     |
[INFO] [stderr] 330 |             let mut phase_score2 = 0.0;
[INFO] [stderr]     |                                    ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `phase_score` is never read
[INFO] [stderr]    --> src/snpfrags.rs:331:35
[INFO] [stderr]     |
[INFO] [stderr] 331 |             let mut phase_score = 0.0;
[INFO] [stderr]     |                                   ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `eta_i`
[INFO] [stderr]    --> src/snpfrags.rs:396:17
[INFO] [stderr]     |
[INFO] [stderr] 396 |             let eta_i = snp.genotype;
[INFO] [stderr]     |                 ^^^^^ help: if this is intentional, prefix it with an underscore: `_eta_i`
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `phase_score` is never read
[INFO] [stderr]    --> src/snpfrags.rs:480:35
[INFO] [stderr]     |
[INFO] [stderr] 480 |             let mut phase_score = 0.0;
[INFO] [stderr]     |                                   ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `q` is never read
[INFO] [stderr]    --> src/snpfrags.rs:577:29
[INFO] [stderr]     |
[INFO] [stderr] 577 |                 let mut q = 0.0;
[INFO] [stderr]     |                             ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `qn` is never read
[INFO] [stderr]    --> src/snpfrags.rs:578:30
[INFO] [stderr]     |
[INFO] [stderr] 578 |                 let mut qn = 0.0;
[INFO] [stderr]     |                              ^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `region`
[INFO] [stderr]    --> src/snpfrags.rs:708:13
[INFO] [stderr]     |
[INFO] [stderr] 708 |         let region = self.region.clone().to_string();
[INFO] [stderr]     |             ^^^^^^ help: if this is intentional, prefix it with an underscore: `_region`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]  --> src/somatic.rs:6:9
[INFO] [stderr]   |
[INFO] [stderr] 6 |     let mut hap1_allele_class;
[INFO] [stderr]   |         ----^^^^^^^^^^^^^^^^^
[INFO] [stderr]   |         |
[INFO] [stderr]   |         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]  --> src/somatic.rs:7:9
[INFO] [stderr]   |
[INFO] [stderr] 7 |     let mut hap2_allele_class;
[INFO] [stderr]   |         ----^^^^^^^^^^^^^^^^^
[INFO] [stderr]   |         |
[INFO] [stderr]   |         help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `cgi`
[INFO] [stderr]    --> src/util.rs:699:29
[INFO] [stderr]     |
[INFO] [stderr] 699 |                         for cgi in 0..cg.len() {
[INFO] [stderr]     |                             ^^^ help: if this is intentional, prefix it with an underscore: `_cgi`
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `gt` is never read
[INFO] [stderr]   --> src/vcf.rs:54:30
[INFO] [stderr]    |
[INFO] [stderr] 54 |                 let mut gt = "0/0";
[INFO] [stderr]    |                              ^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: struct `Exon` is never constructed
[INFO] [stderr]  --> src/exon.rs:4:12
[INFO] [stderr]   |
[INFO] [stderr] 4 | pub struct Exon {
[INFO] [stderr]   |            ^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: method `clean_fragments` is never used
[INFO] [stderr]    --> src/fragment.rs:311:12
[INFO] [stderr]     |
[INFO] [stderr]   9 | impl SNPFrag {
[INFO] [stderr]     | ------------ method in this implementation
[INFO] [stderr] ...
[INFO] [stderr] 311 |     pub fn clean_fragments(&mut self) {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `qki` is never used
[INFO] [stderr]   --> src/phase.rs:14:8
[INFO] [stderr]    |
[INFO] [stderr] 14 | pub fn qki(sigma: i32, delta: i32, alt_fraction: f32, base_allele: i32, error_rate: f64) -> f64 {
[INFO] [stderr]    |        ^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `cal_sigma_delta` is never used
[INFO] [stderr]   --> src/phase.rs:51:8
[INFO] [stderr]    |
[INFO] [stderr] 51 | pub fn cal_sigma_delta(sigma_k: i32, delta: &Vec<i32>, altfrac: &Vec<f32>, ps: &Vec<i32>, probs: &Vec<f64>) -> f64 {
[INFO] [stderr]    |        ^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `cal_delta_sigma` is never used
[INFO] [stderr]   --> src/phase.rs:98:8
[INFO] [stderr]    |
[INFO] [stderr] 98 | pub fn cal_delta_sigma(delta_i: i32, alt_fraction_i: f32, sigma: &Vec<i32>, ps: &Vec<i32>, probs: &Vec<f64>) -> f64 {
[INFO] [stderr]    |        ^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `check_block_new_haplotype_haplotag` is never used
[INFO] [stderr]    --> src/phase.rs:357:8
[INFO] [stderr]     |
[INFO] [stderr] 357 | pub fn check_block_new_haplotype_haplotag(snpfrag: &SNPFrag, updated_haplotype: &HashMap<usize, i32>, updated_haplotag: &HashMap<us...
[INFO] [stderr]     |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `cal_inconsistent_percentage` is never used
[INFO] [stderr]    --> src/phase.rs:401:8
[INFO] [stderr]     |
[INFO] [stderr] 401 | pub fn cal_inconsistent_percentage(delta_i: i32, sigma: &Vec<i32>, ps: &Vec<i32>) -> f64 {
[INFO] [stderr]     |        ^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `get_blocks` is never used
[INFO] [stderr]    --> src/phase.rs:411:8
[INFO] [stderr]     |
[INFO] [stderr] 411 | pub fn get_blocks(block_links: &HashMap<[usize; 2], i32>, weight_threshold: u32) -> (Vec<Vec<usize>>, GraphMap<usize, i32, Undirect...
[INFO] [stderr]     |        ^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: fields `hap1_ref_baseqs`, `hap1_alt_baseqs`, `hap2_ref_baseqs`, and `hap2_alt_baseqs` are never read
[INFO] [stderr]   --> src/snp.rs:10:9
[INFO] [stderr]    |
[INFO] [stderr]  9 | pub struct HapQuals {
[INFO] [stderr]    |            -------- fields in this struct
[INFO] [stderr] 10 |     pub hap1_ref_baseqs: Vec<u8>,
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^
[INFO] [stderr] 11 |     pub hap1_alt_baseqs: Vec<u8>,
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^
[INFO] [stderr] 12 |     pub hap2_ref_baseqs: Vec<u8>,
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^
[INFO] [stderr] 13 |     pub hap2_alt_baseqs: Vec<u8>,
[INFO] [stderr]    |         ^^^^^^^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `HapQuals` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stderr] 
[INFO] [stderr] warning: struct `AlleleClass` is never constructed
[INFO] [stderr]   --> src/snp.rs:17:12
[INFO] [stderr]    |
[INFO] [stderr] 17 | pub struct AlleleClass {
[INFO] [stderr]    |            ^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: fields `somatic`, `somatic_score`, and `hap_quals` are never read
[INFO] [stderr]   --> src/snp.rs:82:9
[INFO] [stderr]    |
[INFO] [stderr] 40 | pub struct CandidateSNP {
[INFO] [stderr]    |            ------------ fields in this struct
[INFO] [stderr] ...
[INFO] [stderr] 82 |     pub somatic: bool,
[INFO] [stderr]    |         ^^^^^^^
[INFO] [stderr] 83 |     // detected somatic mutation by model
[INFO] [stderr] 84 |     pub somatic_score: f64,
[INFO] [stderr]    |         ^^^^^^^^^^^^^
[INFO] [stderr] 85 |     // phred somatic score
[INFO] [stderr] 86 |     pub hap_quals: HapQuals,
[INFO] [stderr]    |         ^^^^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `CandidateSNP` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stderr] 
[INFO] [stderr] warning: method `calculate_LD_R2` is never used
[INFO] [stderr]    --> src/snp.rs:107:12
[INFO] [stderr]     |
[INFO] [stderr] 106 | impl LD_Pair {
[INFO] [stderr]     | ------------ method in this implementation
[INFO] [stderr] 107 |     pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: field `block_id` is never read
[INFO] [stderr]    --> src/snp.rs:243:9
[INFO] [stderr]     |
[INFO] [stderr] 242 | pub struct Block {
[INFO] [stderr]     |            ----- field in this struct
[INFO] [stderr] 243 |     pub block_id: u32,
[INFO] [stderr]     |         ^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: `Block` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stderr] 
[INFO] [stderr] warning: field `phased` is never read
[INFO] [stderr]   --> src/snpfrags.rs:29:9
[INFO] [stderr]    |
[INFO] [stderr] 15 | pub struct SNPFrag {
[INFO] [stderr]    |            ------- field in this struct
[INFO] [stderr] ...
[INFO] [stderr] 29 |     pub phased: bool,
[INFO] [stderr]    |         ^^^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `SNPFrag` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stderr] 
[INFO] [stderr] warning: methods `get_somatic_haplotype_baseqs` and `detect_somatic_by_het` are never used
[INFO] [stderr]    --> src/snpfrags.rs:56:12
[INFO] [stderr]     |
[INFO] [stderr]  55 | impl SNPFrag {
[INFO] [stderr]     | ------------ methods in this implementation
[INFO] [stderr]  56 |     pub fn get_somatic_haplotype_baseqs(&mut self, bam_path: &str, region: &Region, phased_fragments: &HashMap<String, i32>) {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] ...
[INFO] [stderr] 735 |     pub fn detect_somatic_by_het(&mut self, bam_path: &str, region: &Region) {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `calculate_prob_somatic` is never used
[INFO] [stderr]  --> src/somatic.rs:5:8
[INFO] [stderr]   |
[INFO] [stderr] 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<...
[INFO] [stderr]   |        ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: methods `get_main_alleles` and `get_none_ref_count` are never used
[INFO] [stderr]    --> src/util.rs:178:12
[INFO] [stderr]     |
[INFO] [stderr] 129 | impl BaseFreq {
[INFO] [stderr]     | ------------- methods in this implementation
[INFO] [stderr] ...
[INFO] [stderr] 178 |     pub fn get_main_alleles(&self) -> Vec<(char, u32)> {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^
[INFO] [stderr] ...
[INFO] [stderr] 203 |     pub fn get_none_ref_count(&self) -> u32 {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: function `load_vcf` is never used
[INFO] [stderr]    --> src/vcf.rs:309:8
[INFO] [stderr]     |
[INFO] [stderr] 309 | pub fn load_vcf(
[INFO] [stderr]     |        ^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: field `phased` is never read
[INFO] [stderr]    --> src/vcf.rs:397:9
[INFO] [stderr]     |
[INFO] [stderr] 394 | pub struct GenotypeAndQuality {
[INFO] [stderr]     |            ------------------ field in this struct
[INFO] [stderr] ...
[INFO] [stderr] 397 |     pub phased: bool,
[INFO] [stderr]     |         ^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: `GenotypeAndQuality` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stderr] 
[INFO] [stderr] warning: method `init_haplotypes_LD2` should have a snake case name
[INFO] [stderr]    --> src/phase.rs:609:19
[INFO] [stderr]     |
[INFO] [stderr] 609 |     pub unsafe fn init_haplotypes_LD2(&mut self, ld_graph: &GraphMap<usize, i32, Undirected>, ld_weight_threshold: u32) -> HashSet<...
[INFO] [stderr]     |                   ^^^^^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `init_haplotypes_ld2`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: method `calculate_LD_R2` should have a snake case name
[INFO] [stderr]    --> src/snp.rs:107:12
[INFO] [stderr]     |
[INFO] [stderr] 107 |     pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `calculate_ld_r2`
[INFO] [stderr] 
[INFO] [stderr] warning: variable `A` should have a snake case name
[INFO] [stderr]    --> src/snp.rs:107:35
[INFO] [stderr]     |
[INFO] [stderr] 107 |     pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 {
[INFO] [stderr]     |                                   ^ help: convert the identifier to snake case: `a`
[INFO] [stderr] 
[INFO] [stderr] warning: variable `B` should have a snake case name
[INFO] [stderr]    --> src/snp.rs:107:49
[INFO] [stderr]     |
[INFO] [stderr] 107 |     pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 {
[INFO] [stderr]     |                                                 ^ help: convert the identifier to snake case: `b`
[INFO] [stderr] 
[INFO] [stderr] warning: variable `AB` should have a snake case name
[INFO] [stderr]    --> src/snp.rs:110:18
[INFO] [stderr]     |
[INFO] [stderr] 110 |         let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]     |                  ^^ help: convert the identifier to snake case: `ab`
[INFO] [stderr] 
[INFO] [stderr] warning: variable `Ab` should have a snake case name
[INFO] [stderr]    --> src/snp.rs:110:26
[INFO] [stderr]     |
[INFO] [stderr] 110 |         let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]     |                          ^^ help: convert the identifier to snake case: `ab`
[INFO] [stderr] 
[INFO] [stderr] warning: variable `aB` should have a snake case name
[INFO] [stderr]    --> src/snp.rs:110:34
[INFO] [stderr]     |
[INFO] [stderr] 110 |         let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]     |                                  ^^ help: convert the identifier to snake case: `a_b`
[INFO] [stderr] 
[INFO] [stderr] warning: variable `pA` should have a snake case name
[INFO] [stderr]    --> src/snp.rs:111:18
[INFO] [stderr]     |
[INFO] [stderr] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]     |                  ^^ help: convert the identifier to snake case: `p_a`
[INFO] [stderr] 
[INFO] [stderr] warning: variable `pB` should have a snake case name
[INFO] [stderr]    --> src/snp.rs:111:34
[INFO] [stderr]     |
[INFO] [stderr] 111 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]     |                                  ^^ help: convert the identifier to snake case: `p_b`
[INFO] [stderr] 
[INFO] [stderr] warning: variable `A` should have a snake case name
[INFO] [stderr]    --> src/snp.rs:158:32
[INFO] [stderr]     |
[INFO] [stderr] 158 |     pub fn calculate_ld(&self, A: u8, a: u8, B: u8, b: u8) -> (f32, i32) {
[INFO] [stderr]     |                                ^ help: convert the identifier to snake case: `a`
[INFO] [stderr] 
[INFO] [stderr] warning: variable `B` should have a snake case name
[INFO] [stderr]    --> src/snp.rs:158:46
[INFO] [stderr]     |
[INFO] [stderr] 158 |     pub fn calculate_ld(&self, A: u8, a: u8, B: u8, b: u8) -> (f32, i32) {
[INFO] [stderr]     |                                              ^ help: convert the identifier to snake case: `b`
[INFO] [stderr] 
[INFO] [stderr] warning: `longcallR` (bin "longcallR" test) generated 100 warnings (run `cargo fix --bin "longcallR" -p longcallR --tests` to apply 34 suggestions)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.29s
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/longcallR-604628088be1166b)
[INFO] [stdout] 
[INFO] [stdout] running 0 tests
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "89daf6632f9ae8095642b7ce60d9e66d07a6f366fd37927ea22ddc54c5e79ca2", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "89daf6632f9ae8095642b7ce60d9e66d07a6f366fd37927ea22ddc54c5e79ca2", kill_on_drop: false }`
[INFO] [stdout] 89daf6632f9ae8095642b7ce60d9e66d07a6f366fd37927ea22ddc54c5e79ca2
