[INFO] fetching crate longcallR 2.0.1...
[INFO] testing longcallR-2.0.1 against try#33835004928d3bf65db4d4712e1330766263b0bd for pr-155739
[INFO] extracting crate longcallR 2.0.1 into /workspace/builds/worker-3-tc2/source
[INFO] started tweaking crates.io crate longcallR 2.0.1
[INFO] finished tweaking crates.io crate longcallR 2.0.1
[INFO] tweaked toml for crates.io crate longcallR 2.0.1 written to /workspace/builds/worker-3-tc2/source/Cargo.toml
[INFO] validating manifest of crates.io crate longcallR 2.0.1 on toolchain 33835004928d3bf65db4d4712e1330766263b0bd
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+33835004928d3bf65db4d4712e1330766263b0bd" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate crates.io crate longcallR 2.0.1 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" "+33835004928d3bf65db4d4712e1330766263b0bd" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+33835004928d3bf65db4d4712e1330766263b0bd" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 1d256bc2f3c922f9843c11e47ea267014f4f4708b04689fd83a0a7bb15929128
[INFO] running `Command { std: "docker" "start" "-a" "1d256bc2f3c922f9843c11e47ea267014f4f4708b04689fd83a0a7bb15929128", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "1d256bc2f3c922f9843c11e47ea267014f4f4708b04689fd83a0a7bb15929128", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "1d256bc2f3c922f9843c11e47ea267014f4f4708b04689fd83a0a7bb15929128", kill_on_drop: false }`
[INFO] [stdout] 1d256bc2f3c922f9843c11e47ea267014f4f4708b04689fd83a0a7bb15929128
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+33835004928d3bf65db4d4712e1330766263b0bd" "build" "--frozen" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] f80815b5845263850910a6593764c1630d065b995b062d0b1349410689ce985d
[INFO] running `Command { std: "docker" "start" "-a" "f80815b5845263850910a6593764c1630d065b995b062d0b1349410689ce985d", kill_on_drop: false }`
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[INFO] [stderr]    Compiling longcallR v2.0.1 (/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:91:12
[INFO] [stdout]    |
[INFO] [stdout] 91 | 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:250:17
[INFO] [stdout]     |
[INFO] [stdout] 250 |             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:251:17
[INFO] [stdout]     |
[INFO] [stdout] 251 |             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:333:17
[INFO] [stdout]     |
[INFO] [stdout] 333 |             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:247:31
[INFO] [stdout]     |
[INFO] [stdout] 247 |             let mut logprob = [0.0, 0.0, 0.0];
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 296 |             logprob = loglikelihood.clone();
[INFO] [stdout]     |             ------------------------------- `logprob` is overwritten here before the previous value is read
[INFO] [stdout]     |
[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:682:22
[INFO] [stdout]     |
[INFO] [stdout] 682 |                 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:682:36
[INFO] [stdout]     |
[INFO] [stdout] 682 |                 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:682:50
[INFO] [stdout]     |
[INFO] [stdout] 682 |                 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:682:64
[INFO] [stdout]     |
[INFO] [stdout] 682 |                 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:683:22
[INFO] [stdout]     |
[INFO] [stdout] 683 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                      ^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 692 |                     snp1_ref_frac = snp1.allele_freqs[1];
[INFO] [stdout]     |                     ------------------------------------ `snp1_ref_frac` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp1_alt_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:683:41
[INFO] [stdout]     |
[INFO] [stdout] 683 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                                         ^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 694 |                     snp1_alt_frac = snp1.allele_freqs[0];
[INFO] [stdout]     |                     ------------------------------------ `snp1_alt_frac` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp2_ref_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:683:60
[INFO] [stdout]     |
[INFO] [stdout] 683 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 705 |                     snp2_ref_frac = snp2.allele_freqs[1];
[INFO] [stdout]     |                     ------------------------------------ `snp2_ref_frac` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp2_alt_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:683:79
[INFO] [stdout]     |
[INFO] [stdout] 683 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                                                                               ^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 707 |                     snp2_alt_frac = snp2.allele_freqs[0];
[INFO] [stdout]     |                     ------------------------------------ `snp2_alt_frac` is overwritten here before the previous value is 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]    |                               ^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 78 |                 snp_pos = self.candidate_snps[idx].pos;
[INFO] [stdout]    |                 -------------------------------------- `snp_pos` is overwritten here before the previous value is 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/low_frac.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/low_frac.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: 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:639:38
[INFO] [stdout]     |
[INFO] [stdout] 639 |                     let mut weight = 0;
[INFO] [stdout]     |                                      ^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 647 |                         weight = self.allele_pairs.get(&[from_idx, to_idx]).unwrap().weight;
[INFO] [stdout]     |                         ------------------------------------------------------------------- `weight` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `haplotype_genotype_increase` is never read
[INFO] [stdout]    --> src/phase.rs:868:17
[INFO] [stdout]     |
[INFO] [stdout] 868 |                 haplotype_genotype_increase = true;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 964 |                 haplotype_genotype_increase = true;
[INFO] [stdout]     |                 ---------------------------------- `haplotype_genotype_increase` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `max_q` is never read
[INFO] [stdout]    --> src/phase.rs:924:37
[INFO] [stdout]     |
[INFO] [stdout] 924 |                     let mut max_q = 0.0;
[INFO] [stdout]     |                                     ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 933 |                         max_q = q3.max(q4);
[INFO] [stdout]     |                         ------------------ `max_q` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]     --> src/phase.rs:1040:38
[INFO] [stdout]      |
[INFO] [stdout] 1040 |                 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:1040:46
[INFO] [stdout]      |
[INFO] [stdout] 1040 |                 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:1040:38
[INFO] [stdout]      |
[INFO] [stdout] 1040 |                 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:1040:46
[INFO] [stdout]      |
[INFO] [stdout] 1040 |                 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:1040:22
[INFO] [stdout]      |
[INFO] [stdout] 1040 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                      ^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 1054 |                     q1 = cal_delta_eta_sigma_log(delta_i, eta_i, &sigma, &ps, &probs);
[INFO] [stdout]      |                     ----------------------------------------------------------------- `q1` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `q2` is never read
[INFO] [stdout]     --> src/phase.rs:1040:30
[INFO] [stdout]      |
[INFO] [stdout] 1040 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                              ^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 1055 |                     q2 = cal_delta_eta_sigma_log(delta_i, eta_i * (-1), &sigma, &ps, &probs);
[INFO] [stdout]      |                     ------------------------------------------------------------------------ `q2` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/snp.rs:143:13
[INFO] [stdout]     |
[INFO] [stdout] 143 |         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:109:22
[INFO] [stdout]     |
[INFO] [stdout] 109 |         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:109:38
[INFO] [stdout]     |
[INFO] [stdout] 109 |         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:109:14
[INFO] [stdout]     |
[INFO] [stdout] 109 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |              ^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 138 |         pA = AB + Ab; // P(A)
[INFO] [stdout]     |         ------------ `pA` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `pa` is never read
[INFO] [stdout]    --> src/snp.rs:139:9
[INFO] [stdout]     |
[INFO] [stdout] 139 |         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:109:30
[INFO] [stdout]     |
[INFO] [stdout] 109 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                              ^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 140 |         pB = AB + aB; // P(B)
[INFO] [stdout]     |         ------------ `pB` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `pb` is never read
[INFO] [stdout]    --> src/snp.rs:141:9
[INFO] [stdout]     |
[INFO] [stdout] 141 |         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:121:17
[INFO] [stdout]     |
[INFO] [stdout] 121 |             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:120:31
[INFO] [stdout]     |
[INFO] [stdout] 120 |             let mut snp_pos = -1; // pre-computed position of candidate SNPs
[INFO] [stdout]     |                               ^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 137 |                 snp_pos = self.candidate_snps[self.low_frac_snps[idx]].pos;
[INFO] [stdout]     |                 ---------------------------------------------------------- `snp_pos` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:138:17
[INFO] [stdout]     |
[INFO] [stdout] 124 |                 alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                 ---------------------------------------------------------------------- `alleles` is overwritten here before the previous value is read
[INFO] [stdout] ...
[INFO] [stdout] 138 |                 alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:124:17
[INFO] [stdout]     |
[INFO] [stdout] 124 |                 alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 175 |                                     alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                                     ---------------------------------------------------------------------- `alleles` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:175:37
[INFO] [stdout]     |
[INFO] [stdout] 175 | ...                   alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 191 | ...                   alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ---------------------------------------------------------------------- `alleles` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:191:37
[INFO] [stdout]     |
[INFO] [stdout] 191 | ...                   alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 203 | ...                   alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ---------------------------------------------------------------------- `alleles` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:203:37
[INFO] [stdout]     |
[INFO] [stdout] 203 | ...                   alleles = self.candidate_snps[self.low_frac_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:267:36
[INFO] [stdout]     |
[INFO] [stdout] 267 |             let mut phase_score1 = 0.0;
[INFO] [stdout]     |                                    ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 275 |                 phase_score1 = -10.0_f64 * (1.0 - cal_phase_score_log(1, 0, &sigma, &ps, &probs)).log10(); // calaulate assignment ...
[INFO] [stdout]     |                 ----------------------------------------------------------------------------------------- `phase_score1` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score2` is never read
[INFO] [stdout]    --> src/snpfrags.rs:268:36
[INFO] [stdout]     |
[INFO] [stdout] 268 |             let mut phase_score2 = 0.0;
[INFO] [stdout]     |                                    ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 276 |                 phase_score2 = -10.0_f64 * (1.0 - cal_phase_score_log(-1, 0, &sigma, &ps, &probs)).log10(); // calaulate assignment...
[INFO] [stdout]     |                 ------------------------------------------------------------------------------------------ `phase_score2` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score` is never read
[INFO] [stdout]    --> src/snpfrags.rs:269:35
[INFO] [stdout]     |
[INFO] [stdout] 269 |             let mut phase_score = 0.0;
[INFO] [stdout]     |                                   ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 282 |                 phase_score = phase_score1.max(phase_score2);
[INFO] [stdout]     |                 -------------------------------------------- `phase_score` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score1` is never read
[INFO] [stdout]    --> src/snpfrags.rs:355:36
[INFO] [stdout]     |
[INFO] [stdout] 355 |             let mut phase_score1 = 0.0;
[INFO] [stdout]     |                                    ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 363 |                 phase_score1 = -10.0_f64 * (1.0 - cal_phase_score_log(1, 0, &sigma, &ps, &probs)).log10(); // calaulate assignment ...
[INFO] [stdout]     |                 ----------------------------------------------------------------------------------------- `phase_score1` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score2` is never read
[INFO] [stdout]    --> src/snpfrags.rs:356:36
[INFO] [stdout]     |
[INFO] [stdout] 356 |             let mut phase_score2 = 0.0;
[INFO] [stdout]     |                                    ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 364 |                 phase_score2 = -10.0_f64 * (1.0 - cal_phase_score_log(-1, 0, &sigma, &ps, &probs)).log10(); // calaulate assignment...
[INFO] [stdout]     |                 ------------------------------------------------------------------------------------------ `phase_score2` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score` is never read
[INFO] [stdout]    --> src/snpfrags.rs:357:35
[INFO] [stdout]     |
[INFO] [stdout] 357 |             let mut phase_score = 0.0;
[INFO] [stdout]     |                                   ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 370 |                 phase_score = phase_score1.max(phase_score2);
[INFO] [stdout]     |                 -------------------------------------------- `phase_score` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `eta_i`
[INFO] [stdout]    --> src/snpfrags.rs:422:17
[INFO] [stdout]     |
[INFO] [stdout] 422 |             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:506:35
[INFO] [stdout]     |
[INFO] [stdout] 506 | ...   let mut phase_score = 0.0;
[INFO] [stdout]     |                             ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 509 | ...       phase_score = -10.0_f64 * (1.0 - cal_phase_score_log(snp.haplotype, snp.genotype, &sigma, &ps, &probs)).log10(); // calau...
[INFO] [stdout]     |           --------------------------------------------------------------------------------------------------------------- `phase_score` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `q` is never read
[INFO] [stdout]    --> src/snpfrags.rs:604:29
[INFO] [stdout]     |
[INFO] [stdout] 604 |                 let mut q = 0.0;
[INFO] [stdout]     |                             ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 607 |                     q = cal_sigma_delta_eta_log(sigma_k, &delta, &eta, &ps, &probs);
[INFO] [stdout]     |                     --------------------------------------------------------------- `q` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `qn` is never read
[INFO] [stdout]    --> src/snpfrags.rs:605:30
[INFO] [stdout]     |
[INFO] [stdout] 605 |                 let mut qn = 0.0;
[INFO] [stdout]     |                              ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 608 |                     qn = cal_sigma_delta_eta_log(sigma_k * (-1), &delta, &eta, &ps, &probs);
[INFO] [stdout]     |                     ----------------------------------------------------------------------- `qn` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `region`
[INFO] [stdout]    --> src/snpfrags.rs:735:13
[INFO] [stdout]     |
[INFO] [stdout] 735 |         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: unused variable: `cgi`
[INFO] [stdout]    --> src/util.rs:716:29
[INFO] [stdout]     |
[INFO] [stdout] 716 |                         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:53:30
[INFO] [stdout]    |
[INFO] [stdout] 53 |                 let mut gt = "0/0";
[INFO] [stdout]    |                              ^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 59 |                     gt = "1/2"
[INFO] [stdout]    |                     ---------- `gt` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `gt` is never read
[INFO] [stdout]    --> src/vcf.rs:180:30
[INFO] [stdout]     |
[INFO] [stdout] 180 |                 let mut gt = "0/0";
[INFO] [stdout]     |                              ^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 255 |                             gt = "1/2";
[INFO] [stdout]     |                             ---------- `gt` is overwritten here before the previous value is 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 `calculate_prob_low_frac` is never used
[INFO] [stdout]  --> src/low_frac.rs:5:8
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub fn calculate_prob_low_frac(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: 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:402:8
[INFO] [stdout]     |
[INFO] [stdout] 402 | 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:412:8
[INFO] [stdout]     |
[INFO] [stdout] 412 | 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 `low_frac` 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 low_frac: bool,
[INFO] [stdout]    |         ^^^^^^^^
[INFO] [stdout] 83 |     // detected low fraction variant by model
[INFO] [stdout] 84 |     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:105:12
[INFO] [stdout]     |
[INFO] [stdout] 104 | impl LD_Pair {
[INFO] [stdout]     | ------------ method in this implementation
[INFO] [stdout] 105 |     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:241:9
[INFO] [stdout]     |
[INFO] [stdout] 240 | pub struct Block {
[INFO] [stdout]     |            ----- field in this struct
[INFO] [stdout] 241 |     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_low_frac_haplotype_baseqs` and `detect_low_frac_by_het` are never used
[INFO] [stdout]    --> src/snpfrags.rs:90:12
[INFO] [stdout]     |
[INFO] [stdout]  55 | impl SNPFrag {
[INFO] [stdout]     | ------------ methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout]  90 |     pub fn get_low_frac_haplotype_baseqs(&mut self, bam_path: &str, region: &Region, phased_fragments: &HashMap<String, i32>) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 762 |     pub fn detect_low_frac_by_het(&mut self, bam_path: &str, region: &Region) {
[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:179:12
[INFO] [stdout]     |
[INFO] [stdout] 130 | impl BaseFreq {
[INFO] [stdout]     | ------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 179 |     pub fn get_main_alleles(&self) -> Vec<(char, u32)> {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 204 |     pub fn get_none_ref_count(&self) -> u32 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `info` is never read
[INFO] [stdout]   --> src/vcf.rs:21:9
[INFO] [stdout]    |
[INFO] [stdout] 13 | pub struct VCFRecord {
[INFO] [stdout]    |            --------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 21 |     pub info: Vec<u8>,
[INFO] [stdout]    |         ^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `VCFRecord` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `load_vcf` is never used
[INFO] [stdout]    --> src/vcf.rs:313:8
[INFO] [stdout]     |
[INFO] [stdout] 313 | pub fn load_vcf(
[INFO] [stdout]     |        ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `phased` is never read
[INFO] [stdout]    --> src/vcf.rs:407:9
[INFO] [stdout]     |
[INFO] [stdout] 404 | pub struct GenotypeAndQuality {
[INFO] [stdout]     |            ------------------ field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 407 |     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:610:19
[INFO] [stdout]     |
[INFO] [stdout] 610 |     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:105:12
[INFO] [stdout]     |
[INFO] [stdout] 105 |     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:105:35
[INFO] [stdout]     |
[INFO] [stdout] 105 |     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:105:49
[INFO] [stdout]     |
[INFO] [stdout] 105 |     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:108:18
[INFO] [stdout]     |
[INFO] [stdout] 108 |         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:108:26
[INFO] [stdout]     |
[INFO] [stdout] 108 |         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:108:34
[INFO] [stdout]     |
[INFO] [stdout] 108 |         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:109:18
[INFO] [stdout]     |
[INFO] [stdout] 109 |         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:109:34
[INFO] [stdout]     |
[INFO] [stdout] 109 |         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:156:32
[INFO] [stdout]     |
[INFO] [stdout] 156 |     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:156:46
[INFO] [stdout]     |
[INFO] [stdout] 156 |     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 43.83s
[INFO] running `Command { std: "docker" "inspect" "f80815b5845263850910a6593764c1630d065b995b062d0b1349410689ce985d", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "f80815b5845263850910a6593764c1630d065b995b062d0b1349410689ce985d", kill_on_drop: false }`
[INFO] [stdout] f80815b5845263850910a6593764c1630d065b995b062d0b1349410689ce985d
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+33835004928d3bf65db4d4712e1330766263b0bd" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 71c5aae02b8518225f5e6caf0bddf6ca6bde0af86c982f61106171c08769a41a
[INFO] running `Command { std: "docker" "start" "-a" "71c5aae02b8518225f5e6caf0bddf6ca6bde0af86c982f61106171c08769a41a", kill_on_drop: false }`
[INFO] [stderr]    Compiling longcallR v2.0.1 (/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:91:12
[INFO] [stdout]    |
[INFO] [stdout] 91 | 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:250:17
[INFO] [stdout]     |
[INFO] [stdout] 250 |             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:251:17
[INFO] [stdout]     |
[INFO] [stdout] 251 |             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:333:17
[INFO] [stdout]     |
[INFO] [stdout] 333 |             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:247:31
[INFO] [stdout]     |
[INFO] [stdout] 247 |             let mut logprob = [0.0, 0.0, 0.0];
[INFO] [stdout]     |                               ^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 296 |             logprob = loglikelihood.clone();
[INFO] [stdout]     |             ------------------------------- `logprob` is overwritten here before the previous value is read
[INFO] [stdout]     |
[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:682:22
[INFO] [stdout]     |
[INFO] [stdout] 682 |                 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:682:36
[INFO] [stdout]     |
[INFO] [stdout] 682 |                 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:682:50
[INFO] [stdout]     |
[INFO] [stdout] 682 |                 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:682:64
[INFO] [stdout]     |
[INFO] [stdout] 682 |                 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:683:22
[INFO] [stdout]     |
[INFO] [stdout] 683 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                      ^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 692 |                     snp1_ref_frac = snp1.allele_freqs[1];
[INFO] [stdout]     |                     ------------------------------------ `snp1_ref_frac` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp1_alt_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:683:41
[INFO] [stdout]     |
[INFO] [stdout] 683 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                                         ^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 694 |                     snp1_alt_frac = snp1.allele_freqs[0];
[INFO] [stdout]     |                     ------------------------------------ `snp1_alt_frac` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp2_ref_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:683:60
[INFO] [stdout]     |
[INFO] [stdout] 683 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                                                            ^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 705 |                     snp2_ref_frac = snp2.allele_freqs[1];
[INFO] [stdout]     |                     ------------------------------------ `snp2_ref_frac` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `snp2_alt_frac` is never read
[INFO] [stdout]    --> src/candidate.rs:683:79
[INFO] [stdout]     |
[INFO] [stdout] 683 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stdout]     |                                                                               ^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 707 |                     snp2_alt_frac = snp2.allele_freqs[0];
[INFO] [stdout]     |                     ------------------------------------ `snp2_alt_frac` is overwritten here before the previous value is 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]    |                               ^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 78 |                 snp_pos = self.candidate_snps[idx].pos;
[INFO] [stdout]    |                 -------------------------------------- `snp_pos` is overwritten here before the previous value is 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/low_frac.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/low_frac.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: 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:639:38
[INFO] [stdout]     |
[INFO] [stdout] 639 |                     let mut weight = 0;
[INFO] [stdout]     |                                      ^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 647 |                         weight = self.allele_pairs.get(&[from_idx, to_idx]).unwrap().weight;
[INFO] [stdout]     |                         ------------------------------------------------------------------- `weight` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `haplotype_genotype_increase` is never read
[INFO] [stdout]    --> src/phase.rs:868:17
[INFO] [stdout]     |
[INFO] [stdout] 868 |                 haplotype_genotype_increase = true;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 964 |                 haplotype_genotype_increase = true;
[INFO] [stdout]     |                 ---------------------------------- `haplotype_genotype_increase` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `max_q` is never read
[INFO] [stdout]    --> src/phase.rs:924:37
[INFO] [stdout]     |
[INFO] [stdout] 924 |                     let mut max_q = 0.0;
[INFO] [stdout]     |                                     ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 933 |                         max_q = q3.max(q4);
[INFO] [stdout]     |                         ------------------ `max_q` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]     --> src/phase.rs:1040:38
[INFO] [stdout]      |
[INFO] [stdout] 1040 |                 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:1040:46
[INFO] [stdout]      |
[INFO] [stdout] 1040 |                 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:1040:38
[INFO] [stdout]      |
[INFO] [stdout] 1040 |                 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:1040:46
[INFO] [stdout]      |
[INFO] [stdout] 1040 |                 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:1040:22
[INFO] [stdout]      |
[INFO] [stdout] 1040 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                      ^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 1054 |                     q1 = cal_delta_eta_sigma_log(delta_i, eta_i, &sigma, &ps, &probs);
[INFO] [stdout]      |                     ----------------------------------------------------------------- `q1` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `q2` is never read
[INFO] [stdout]     --> src/phase.rs:1040:30
[INFO] [stdout]      |
[INFO] [stdout] 1040 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]      |                              ^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 1055 |                     q2 = cal_delta_eta_sigma_log(delta_i, eta_i * (-1), &sigma, &ps, &probs);
[INFO] [stdout]      |                     ------------------------------------------------------------------------ `q2` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/snp.rs:143:13
[INFO] [stdout]     |
[INFO] [stdout] 143 |         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:109:22
[INFO] [stdout]     |
[INFO] [stdout] 109 |         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:109:38
[INFO] [stdout]     |
[INFO] [stdout] 109 |         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:109:14
[INFO] [stdout]     |
[INFO] [stdout] 109 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |              ^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 138 |         pA = AB + Ab; // P(A)
[INFO] [stdout]     |         ------------ `pA` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `pa` is never read
[INFO] [stdout]    --> src/snp.rs:139:9
[INFO] [stdout]     |
[INFO] [stdout] 139 |         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:109:30
[INFO] [stdout]     |
[INFO] [stdout] 109 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stdout]     |                              ^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 140 |         pB = AB + aB; // P(B)
[INFO] [stdout]     |         ------------ `pB` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `pb` is never read
[INFO] [stdout]    --> src/snp.rs:141:9
[INFO] [stdout]     |
[INFO] [stdout] 141 |         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:121:17
[INFO] [stdout]     |
[INFO] [stdout] 121 |             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:120:31
[INFO] [stdout]     |
[INFO] [stdout] 120 |             let mut snp_pos = -1; // pre-computed position of candidate SNPs
[INFO] [stdout]     |                               ^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 137 |                 snp_pos = self.candidate_snps[self.low_frac_snps[idx]].pos;
[INFO] [stdout]     |                 ---------------------------------------------------------- `snp_pos` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:138:17
[INFO] [stdout]     |
[INFO] [stdout] 124 |                 alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                 ---------------------------------------------------------------------- `alleles` is overwritten here before the previous value is read
[INFO] [stdout] ...
[INFO] [stdout] 138 |                 alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:124:17
[INFO] [stdout]     |
[INFO] [stdout] 124 |                 alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 175 |                                     alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                                     ---------------------------------------------------------------------- `alleles` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:175:37
[INFO] [stdout]     |
[INFO] [stdout] 175 | ...                   alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 191 | ...                   alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ---------------------------------------------------------------------- `alleles` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:191:37
[INFO] [stdout]     |
[INFO] [stdout] 191 | ...                   alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 203 | ...                   alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stdout]     |                       ---------------------------------------------------------------------- `alleles` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `alleles` is never read
[INFO] [stdout]    --> src/snpfrags.rs:203:37
[INFO] [stdout]     |
[INFO] [stdout] 203 | ...                   alleles = self.candidate_snps[self.low_frac_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:267:36
[INFO] [stdout]     |
[INFO] [stdout] 267 |             let mut phase_score1 = 0.0;
[INFO] [stdout]     |                                    ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 275 |                 phase_score1 = -10.0_f64 * (1.0 - cal_phase_score_log(1, 0, &sigma, &ps, &probs)).log10(); // calaulate assignment ...
[INFO] [stdout]     |                 ----------------------------------------------------------------------------------------- `phase_score1` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score2` is never read
[INFO] [stdout]    --> src/snpfrags.rs:268:36
[INFO] [stdout]     |
[INFO] [stdout] 268 |             let mut phase_score2 = 0.0;
[INFO] [stdout]     |                                    ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 276 |                 phase_score2 = -10.0_f64 * (1.0 - cal_phase_score_log(-1, 0, &sigma, &ps, &probs)).log10(); // calaulate assignment...
[INFO] [stdout]     |                 ------------------------------------------------------------------------------------------ `phase_score2` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score` is never read
[INFO] [stdout]    --> src/snpfrags.rs:269:35
[INFO] [stdout]     |
[INFO] [stdout] 269 |             let mut phase_score = 0.0;
[INFO] [stdout]     |                                   ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 282 |                 phase_score = phase_score1.max(phase_score2);
[INFO] [stdout]     |                 -------------------------------------------- `phase_score` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score1` is never read
[INFO] [stdout]    --> src/snpfrags.rs:355:36
[INFO] [stdout]     |
[INFO] [stdout] 355 |             let mut phase_score1 = 0.0;
[INFO] [stdout]     |                                    ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 363 |                 phase_score1 = -10.0_f64 * (1.0 - cal_phase_score_log(1, 0, &sigma, &ps, &probs)).log10(); // calaulate assignment ...
[INFO] [stdout]     |                 ----------------------------------------------------------------------------------------- `phase_score1` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score2` is never read
[INFO] [stdout]    --> src/snpfrags.rs:356:36
[INFO] [stdout]     |
[INFO] [stdout] 356 |             let mut phase_score2 = 0.0;
[INFO] [stdout]     |                                    ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 364 |                 phase_score2 = -10.0_f64 * (1.0 - cal_phase_score_log(-1, 0, &sigma, &ps, &probs)).log10(); // calaulate assignment...
[INFO] [stdout]     |                 ------------------------------------------------------------------------------------------ `phase_score2` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `phase_score` is never read
[INFO] [stdout]    --> src/snpfrags.rs:357:35
[INFO] [stdout]     |
[INFO] [stdout] 357 |             let mut phase_score = 0.0;
[INFO] [stdout]     |                                   ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 370 |                 phase_score = phase_score1.max(phase_score2);
[INFO] [stdout]     |                 -------------------------------------------- `phase_score` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `eta_i`
[INFO] [stdout]    --> src/snpfrags.rs:422:17
[INFO] [stdout]     |
[INFO] [stdout] 422 |             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:506:35
[INFO] [stdout]     |
[INFO] [stdout] 506 | ...   let mut phase_score = 0.0;
[INFO] [stdout]     |                             ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 509 | ...       phase_score = -10.0_f64 * (1.0 - cal_phase_score_log(snp.haplotype, snp.genotype, &sigma, &ps, &probs)).log10(); // calau...
[INFO] [stdout]     |           --------------------------------------------------------------------------------------------------------------- `phase_score` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `q` is never read
[INFO] [stdout]    --> src/snpfrags.rs:604:29
[INFO] [stdout]     |
[INFO] [stdout] 604 |                 let mut q = 0.0;
[INFO] [stdout]     |                             ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 607 |                     q = cal_sigma_delta_eta_log(sigma_k, &delta, &eta, &ps, &probs);
[INFO] [stdout]     |                     --------------------------------------------------------------- `q` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `qn` is never read
[INFO] [stdout]    --> src/snpfrags.rs:605:30
[INFO] [stdout]     |
[INFO] [stdout] 605 |                 let mut qn = 0.0;
[INFO] [stdout]     |                              ^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 608 |                     qn = cal_sigma_delta_eta_log(sigma_k * (-1), &delta, &eta, &ps, &probs);
[INFO] [stdout]     |                     ----------------------------------------------------------------------- `qn` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `region`
[INFO] [stdout]    --> src/snpfrags.rs:735:13
[INFO] [stdout]     |
[INFO] [stdout] 735 |         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: unused variable: `cgi`
[INFO] [stdout]    --> src/util.rs:716:29
[INFO] [stdout]     |
[INFO] [stdout] 716 |                         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:53:30
[INFO] [stdout]    |
[INFO] [stdout] 53 |                 let mut gt = "0/0";
[INFO] [stdout]    |                              ^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 59 |                     gt = "1/2"
[INFO] [stdout]    |                     ---------- `gt` is overwritten here before the previous value is read
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `gt` is never read
[INFO] [stdout]    --> src/vcf.rs:180:30
[INFO] [stdout]     |
[INFO] [stdout] 180 |                 let mut gt = "0/0";
[INFO] [stdout]     |                              ^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 255 |                             gt = "1/2";
[INFO] [stdout]     |                             ---------- `gt` is overwritten here before the previous value is 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 `calculate_prob_low_frac` is never used
[INFO] [stdout]  --> src/low_frac.rs:5:8
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub fn calculate_prob_low_frac(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: 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:402:8
[INFO] [stdout]     |
[INFO] [stdout] 402 | 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:412:8
[INFO] [stdout]     |
[INFO] [stdout] 412 | 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 `low_frac` 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 low_frac: bool,
[INFO] [stdout]    |         ^^^^^^^^
[INFO] [stdout] 83 |     // detected low fraction variant by model
[INFO] [stdout] 84 |     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:105:12
[INFO] [stdout]     |
[INFO] [stdout] 104 | impl LD_Pair {
[INFO] [stdout]     | ------------ method in this implementation
[INFO] [stdout] 105 |     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:241:9
[INFO] [stdout]     |
[INFO] [stdout] 240 | pub struct Block {
[INFO] [stdout]     |            ----- field in this struct
[INFO] [stdout] 241 |     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_low_frac_haplotype_baseqs` and `detect_low_frac_by_het` are never used
[INFO] [stdout]    --> src/snpfrags.rs:90:12
[INFO] [stdout]     |
[INFO] [stdout]  55 | impl SNPFrag {
[INFO] [stdout]     | ------------ methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout]  90 |     pub fn get_low_frac_haplotype_baseqs(&mut self, bam_path: &str, region: &Region, phased_fragments: &HashMap<String, i32>) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 762 |     pub fn detect_low_frac_by_het(&mut self, bam_path: &str, region: &Region) {
[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:179:12
[INFO] [stdout]     |
[INFO] [stdout] 130 | impl BaseFreq {
[INFO] [stdout]     | ------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 179 |     pub fn get_main_alleles(&self) -> Vec<(char, u32)> {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 204 |     pub fn get_none_ref_count(&self) -> u32 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `info` is never read
[INFO] [stdout]   --> src/vcf.rs:21:9
[INFO] [stdout]    |
[INFO] [stdout] 13 | pub struct VCFRecord {
[INFO] [stdout]    |            --------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 21 |     pub info: Vec<u8>,
[INFO] [stdout]    |         ^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `VCFRecord` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: function `load_vcf` is never used
[INFO] [stdout]    --> src/vcf.rs:313:8
[INFO] [stdout]     |
[INFO] [stdout] 313 | pub fn load_vcf(
[INFO] [stdout]     |        ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `phased` is never read
[INFO] [stdout]    --> src/vcf.rs:407:9
[INFO] [stdout]     |
[INFO] [stdout] 404 | pub struct GenotypeAndQuality {
[INFO] [stdout]     |            ------------------ field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 407 |     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:610:19
[INFO] [stdout]     |
[INFO] [stdout] 610 |     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:105:12
[INFO] [stdout]     |
[INFO] [stdout] 105 |     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:105:35
[INFO] [stdout]     |
[INFO] [stdout] 105 |     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:105:49
[INFO] [stdout]     |
[INFO] [stdout] 105 |     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:108:18
[INFO] [stdout]     |
[INFO] [stdout] 108 |         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:108:26
[INFO] [stdout]     |
[INFO] [stdout] 108 |         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:108:34
[INFO] [stdout]     |
[INFO] [stdout] 108 |         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:109:18
[INFO] [stdout]     |
[INFO] [stdout] 109 |         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:109:34
[INFO] [stdout]     |
[INFO] [stdout] 109 |         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:156:32
[INFO] [stdout]     |
[INFO] [stdout] 156 |     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:156:46
[INFO] [stdout]     |
[INFO] [stdout] 156 |     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 2.08s
[INFO] running `Command { std: "docker" "inspect" "71c5aae02b8518225f5e6caf0bddf6ca6bde0af86c982f61106171c08769a41a", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "71c5aae02b8518225f5e6caf0bddf6ca6bde0af86c982f61106171c08769a41a", kill_on_drop: false }`
[INFO] [stdout] 71c5aae02b8518225f5e6caf0bddf6ca6bde0af86c982f61106171c08769a41a
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-3-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+33835004928d3bf65db4d4712e1330766263b0bd" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] f0507c674910fff182d20f69f04331a70ecbd99a678bfa57d40637d9d67a0127
[INFO] running `Command { std: "docker" "start" "-a" "f0507c674910fff182d20f69f04331a70ecbd99a678bfa57d40637d9d67a0127", 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:91:12
[INFO] [stderr]    |
[INFO] [stderr] 91 | 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:250:17
[INFO] [stderr]     |
[INFO] [stderr] 250 |             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:251:17
[INFO] [stderr]     |
[INFO] [stderr] 251 |             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:333:17
[INFO] [stderr]     |
[INFO] [stderr] 333 |             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:247:31
[INFO] [stderr]     |
[INFO] [stderr] 247 |             let mut logprob = [0.0, 0.0, 0.0];
[INFO] [stderr]     |                               ^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 296 |             logprob = loglikelihood.clone();
[INFO] [stderr]     |             ------------------------------- `logprob` is overwritten here before the previous value is read
[INFO] [stderr]     |
[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:682:22
[INFO] [stderr]     |
[INFO] [stderr] 682 |                 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:682:36
[INFO] [stderr]     |
[INFO] [stderr] 682 |                 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:682:50
[INFO] [stderr]     |
[INFO] [stderr] 682 |                 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:682:64
[INFO] [stderr]     |
[INFO] [stderr] 682 |                 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:683:22
[INFO] [stderr]     |
[INFO] [stderr] 683 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stderr]     |                      ^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 692 |                     snp1_ref_frac = snp1.allele_freqs[1];
[INFO] [stderr]     |                     ------------------------------------ `snp1_ref_frac` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `snp1_alt_frac` is never read
[INFO] [stderr]    --> src/candidate.rs:683:41
[INFO] [stderr]     |
[INFO] [stderr] 683 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stderr]     |                                         ^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 694 |                     snp1_alt_frac = snp1.allele_freqs[0];
[INFO] [stderr]     |                     ------------------------------------ `snp1_alt_frac` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `snp2_ref_frac` is never read
[INFO] [stderr]    --> src/candidate.rs:683:60
[INFO] [stderr]     |
[INFO] [stderr] 683 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stderr]     |                                                            ^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 705 |                     snp2_ref_frac = snp2.allele_freqs[1];
[INFO] [stderr]     |                     ------------------------------------ `snp2_ref_frac` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `snp2_alt_frac` is never read
[INFO] [stderr]    --> src/candidate.rs:683:79
[INFO] [stderr]     |
[INFO] [stderr] 683 |                 let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) =
[INFO] [stderr]     |                                                                               ^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 707 |                     snp2_alt_frac = snp2.allele_freqs[0];
[INFO] [stderr]     |                     ------------------------------------ `snp2_alt_frac` is overwritten here before the previous value is 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]    |                               ^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 78 |                 snp_pos = self.candidate_snps[idx].pos;
[INFO] [stderr]    |                 -------------------------------------- `snp_pos` is overwritten here before the previous value is 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/low_frac.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/low_frac.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: 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:639:38
[INFO] [stderr]     |
[INFO] [stderr] 639 |                     let mut weight = 0;
[INFO] [stderr]     |                                      ^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 647 |                         weight = self.allele_pairs.get(&[from_idx, to_idx]).unwrap().weight;
[INFO] [stderr]     |                         ------------------------------------------------------------------- `weight` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `haplotype_genotype_increase` is never read
[INFO] [stderr]    --> src/phase.rs:868:17
[INFO] [stderr]     |
[INFO] [stderr] 868 |                 haplotype_genotype_increase = true;
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 964 |                 haplotype_genotype_increase = true;
[INFO] [stderr]     |                 ---------------------------------- `haplotype_genotype_increase` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `max_q` is never read
[INFO] [stderr]    --> src/phase.rs:924:37
[INFO] [stderr]     |
[INFO] [stderr] 924 |                     let mut max_q = 0.0;
[INFO] [stderr]     |                                     ^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 933 |                         max_q = q3.max(q4);
[INFO] [stderr]     |                         ------------------ `max_q` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]     --> src/phase.rs:1040:38
[INFO] [stderr]      |
[INFO] [stderr] 1040 |                 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:1040:46
[INFO] [stderr]      |
[INFO] [stderr] 1040 |                 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:1040:38
[INFO] [stderr]      |
[INFO] [stderr] 1040 |                 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:1040:46
[INFO] [stderr]      |
[INFO] [stderr] 1040 |                 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:1040:22
[INFO] [stderr]      |
[INFO] [stderr] 1040 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]      |                      ^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 1054 |                     q1 = cal_delta_eta_sigma_log(delta_i, eta_i, &sigma, &ps, &probs);
[INFO] [stderr]      |                     ----------------------------------------------------------------- `q1` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `q2` is never read
[INFO] [stderr]     --> src/phase.rs:1040:30
[INFO] [stderr]      |
[INFO] [stderr] 1040 |                 let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]      |                              ^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 1055 |                     q2 = cal_delta_eta_sigma_log(delta_i, eta_i * (-1), &sigma, &ps, &probs);
[INFO] [stderr]      |                     ------------------------------------------------------------------------ `q2` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/snp.rs:143:13
[INFO] [stderr]     |
[INFO] [stderr] 143 |         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:109:22
[INFO] [stderr]     |
[INFO] [stderr] 109 |         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:109:38
[INFO] [stderr]     |
[INFO] [stderr] 109 |         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:109:14
[INFO] [stderr]     |
[INFO] [stderr] 109 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]     |              ^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 138 |         pA = AB + Ab; // P(A)
[INFO] [stderr]     |         ------------ `pA` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `pa` is never read
[INFO] [stderr]    --> src/snp.rs:139:9
[INFO] [stderr]     |
[INFO] [stderr] 139 |         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:109:30
[INFO] [stderr]     |
[INFO] [stderr] 109 |         let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0);
[INFO] [stderr]     |                              ^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 140 |         pB = AB + aB; // P(B)
[INFO] [stderr]     |         ------------ `pB` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `pb` is never read
[INFO] [stderr]    --> src/snp.rs:141:9
[INFO] [stderr]     |
[INFO] [stderr] 141 |         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:121:17
[INFO] [stderr]     |
[INFO] [stderr] 121 |             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:120:31
[INFO] [stderr]     |
[INFO] [stderr] 120 |             let mut snp_pos = -1; // pre-computed position of candidate SNPs
[INFO] [stderr]     |                               ^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 137 |                 snp_pos = self.candidate_snps[self.low_frac_snps[idx]].pos;
[INFO] [stderr]     |                 ---------------------------------------------------------- `snp_pos` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `alleles` is never read
[INFO] [stderr]    --> src/snpfrags.rs:138:17
[INFO] [stderr]     |
[INFO] [stderr] 124 |                 alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stderr]     |                 ---------------------------------------------------------------------- `alleles` is overwritten here before the previous value is read
[INFO] [stderr] ...
[INFO] [stderr] 138 |                 alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `alleles` is never read
[INFO] [stderr]    --> src/snpfrags.rs:124:17
[INFO] [stderr]     |
[INFO] [stderr] 124 |                 alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 175 |                                     alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stderr]     |                                     ---------------------------------------------------------------------- `alleles` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `alleles` is never read
[INFO] [stderr]    --> src/snpfrags.rs:175:37
[INFO] [stderr]     |
[INFO] [stderr] 175 | ...                   alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stderr]     |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 191 | ...                   alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stderr]     |                       ---------------------------------------------------------------------- `alleles` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `alleles` is never read
[INFO] [stderr]    --> src/snpfrags.rs:191:37
[INFO] [stderr]     |
[INFO] [stderr] 191 | ...                   alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stderr]     |                       ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 203 | ...                   alleles = self.candidate_snps[self.low_frac_snps[idx]].alleles.clone();
[INFO] [stderr]     |                       ---------------------------------------------------------------------- `alleles` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `alleles` is never read
[INFO] [stderr]    --> src/snpfrags.rs:203:37
[INFO] [stderr]     |
[INFO] [stderr] 203 | ...                   alleles = self.candidate_snps[self.low_frac_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:267:36
[INFO] [stderr]     |
[INFO] [stderr] 267 |             let mut phase_score1 = 0.0;
[INFO] [stderr]     |                                    ^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 275 |                 phase_score1 = -10.0_f64 * (1.0 - cal_phase_score_log(1, 0, &sigma, &ps, &probs)).log10(); // calaulate assignment ...
[INFO] [stderr]     |                 ----------------------------------------------------------------------------------------- `phase_score1` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `phase_score2` is never read
[INFO] [stderr]    --> src/snpfrags.rs:268:36
[INFO] [stderr]     |
[INFO] [stderr] 268 |             let mut phase_score2 = 0.0;
[INFO] [stderr]     |                                    ^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 276 |                 phase_score2 = -10.0_f64 * (1.0 - cal_phase_score_log(-1, 0, &sigma, &ps, &probs)).log10(); // calaulate assignment...
[INFO] [stderr]     |                 ------------------------------------------------------------------------------------------ `phase_score2` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `phase_score` is never read
[INFO] [stderr]    --> src/snpfrags.rs:269:35
[INFO] [stderr]     |
[INFO] [stderr] 269 |             let mut phase_score = 0.0;
[INFO] [stderr]     |                                   ^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 282 |                 phase_score = phase_score1.max(phase_score2);
[INFO] [stderr]     |                 -------------------------------------------- `phase_score` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `phase_score1` is never read
[INFO] [stderr]    --> src/snpfrags.rs:355:36
[INFO] [stderr]     |
[INFO] [stderr] 355 |             let mut phase_score1 = 0.0;
[INFO] [stderr]     |                                    ^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 363 |                 phase_score1 = -10.0_f64 * (1.0 - cal_phase_score_log(1, 0, &sigma, &ps, &probs)).log10(); // calaulate assignment ...
[INFO] [stderr]     |                 ----------------------------------------------------------------------------------------- `phase_score1` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `phase_score2` is never read
[INFO] [stderr]    --> src/snpfrags.rs:356:36
[INFO] [stderr]     |
[INFO] [stderr] 356 |             let mut phase_score2 = 0.0;
[INFO] [stderr]     |                                    ^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 364 |                 phase_score2 = -10.0_f64 * (1.0 - cal_phase_score_log(-1, 0, &sigma, &ps, &probs)).log10(); // calaulate assignment...
[INFO] [stderr]     |                 ------------------------------------------------------------------------------------------ `phase_score2` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `phase_score` is never read
[INFO] [stderr]    --> src/snpfrags.rs:357:35
[INFO] [stderr]     |
[INFO] [stderr] 357 |             let mut phase_score = 0.0;
[INFO] [stderr]     |                                   ^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 370 |                 phase_score = phase_score1.max(phase_score2);
[INFO] [stderr]     |                 -------------------------------------------- `phase_score` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `eta_i`
[INFO] [stderr]    --> src/snpfrags.rs:422:17
[INFO] [stderr]     |
[INFO] [stderr] 422 |             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:506:35
[INFO] [stderr]     |
[INFO] [stderr] 506 | ...   let mut phase_score = 0.0;
[INFO] [stderr]     |                             ^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 509 | ...       phase_score = -10.0_f64 * (1.0 - cal_phase_score_log(snp.haplotype, snp.genotype, &sigma, &ps, &probs)).log10(); // calau...
[INFO] [stderr]     |           --------------------------------------------------------------------------------------------------------------- `phase_score` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `q` is never read
[INFO] [stderr]    --> src/snpfrags.rs:604:29
[INFO] [stderr]     |
[INFO] [stderr] 604 |                 let mut q = 0.0;
[INFO] [stderr]     |                             ^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 607 |                     q = cal_sigma_delta_eta_log(sigma_k, &delta, &eta, &ps, &probs);
[INFO] [stderr]     |                     --------------------------------------------------------------- `q` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `qn` is never read
[INFO] [stderr]    --> src/snpfrags.rs:605:30
[INFO] [stderr]     |
[INFO] [stderr] 605 |                 let mut qn = 0.0;
[INFO] [stderr]     |                              ^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 608 |                     qn = cal_sigma_delta_eta_log(sigma_k * (-1), &delta, &eta, &ps, &probs);
[INFO] [stderr]     |                     ----------------------------------------------------------------------- `qn` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `region`
[INFO] [stderr]    --> src/snpfrags.rs:735:13
[INFO] [stderr]     |
[INFO] [stderr] 735 |         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: unused variable: `cgi`
[INFO] [stderr]    --> src/util.rs:716:29
[INFO] [stderr]     |
[INFO] [stderr] 716 |                         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:53:30
[INFO] [stderr]    |
[INFO] [stderr] 53 |                 let mut gt = "0/0";
[INFO] [stderr]    |                              ^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 59 |                     gt = "1/2"
[INFO] [stderr]    |                     ---------- `gt` is overwritten here before the previous value is read
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `gt` is never read
[INFO] [stderr]    --> src/vcf.rs:180:30
[INFO] [stderr]     |
[INFO] [stderr] 180 |                 let mut gt = "0/0";
[INFO] [stderr]     |                              ^^^^^ this value is reassigned later and never used
[INFO] [stderr] ...
[INFO] [stderr] 255 |                             gt = "1/2";
[INFO] [stderr]     |                             ---------- `gt` is overwritten here before the previous value is 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 `calculate_prob_low_frac` is never used
[INFO] [stderr]  --> src/low_frac.rs:5:8
[INFO] [stderr]   |
[INFO] [stderr] 5 | pub fn calculate_prob_low_frac(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: 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:402:8
[INFO] [stderr]     |
[INFO] [stderr] 402 | 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:412:8
[INFO] [stderr]     |
[INFO] [stderr] 412 | 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 `low_frac` 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 low_frac: bool,
[INFO] [stderr]    |         ^^^^^^^^
[INFO] [stderr] 83 |     // detected low fraction variant by model
[INFO] [stderr] 84 |     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:105:12
[INFO] [stderr]     |
[INFO] [stderr] 104 | impl LD_Pair {
[INFO] [stderr]     | ------------ method in this implementation
[INFO] [stderr] 105 |     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:241:9
[INFO] [stderr]     |
[INFO] [stderr] 240 | pub struct Block {
[INFO] [stderr]     |            ----- field in this struct
[INFO] [stderr] 241 |     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_low_frac_haplotype_baseqs` and `detect_low_frac_by_het` are never used
[INFO] [stderr]    --> src/snpfrags.rs:90:12
[INFO] [stderr]     |
[INFO] [stderr]  55 | impl SNPFrag {
[INFO] [stderr]     | ------------ methods in this implementation
[INFO] [stderr] ...
[INFO] [stderr]  90 |     pub fn get_low_frac_haplotype_baseqs(&mut self, bam_path: &str, region: &Region, phased_fragments: &HashMap<String, i32>) {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] ...
[INFO] [stderr] 762 |     pub fn detect_low_frac_by_het(&mut self, bam_path: &str, region: &Region) {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: methods `get_main_alleles` and `get_none_ref_count` are never used
[INFO] [stderr]    --> src/util.rs:179:12
[INFO] [stderr]     |
[INFO] [stderr] 130 | impl BaseFreq {
[INFO] [stderr]     | ------------- methods in this implementation
[INFO] [stderr] ...
[INFO] [stderr] 179 |     pub fn get_main_alleles(&self) -> Vec<(char, u32)> {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^
[INFO] [stderr] ...
[INFO] [stderr] 204 |     pub fn get_none_ref_count(&self) -> u32 {
[INFO] [stderr]     |            ^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: field `info` is never read
[INFO] [stderr]   --> src/vcf.rs:21:9
[INFO] [stderr]    |
[INFO] [stderr] 13 | pub struct VCFRecord {
[INFO] [stderr]    |            --------- field in this struct
[INFO] [stderr] ...
[INFO] [stderr] 21 |     pub info: Vec<u8>,
[INFO] [stderr]    |         ^^^^
[INFO] [stderr]    |
[INFO] [stderr]    = note: `VCFRecord` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stderr] 
[INFO] [stderr] warning: function `load_vcf` is never used
[INFO] [stderr]    --> src/vcf.rs:313:8
[INFO] [stderr]     |
[INFO] [stderr] 313 | pub fn load_vcf(
[INFO] [stderr]     |        ^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: field `phased` is never read
[INFO] [stderr]    --> src/vcf.rs:407:9
[INFO] [stderr]     |
[INFO] [stderr] 404 | pub struct GenotypeAndQuality {
[INFO] [stderr]     |            ------------------ field in this struct
[INFO] [stderr] ...
[INFO] [stderr] 407 |     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:610:19
[INFO] [stderr]     |
[INFO] [stderr] 610 |     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:105:12
[INFO] [stderr]     |
[INFO] [stderr] 105 |     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:105:35
[INFO] [stderr]     |
[INFO] [stderr] 105 |     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:105:49
[INFO] [stderr]     |
[INFO] [stderr] 105 |     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:108:18
[INFO] [stderr]     |
[INFO] [stderr] 108 |         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:108:26
[INFO] [stderr]     |
[INFO] [stderr] 108 |         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:108:34
[INFO] [stderr]     |
[INFO] [stderr] 108 |         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:109:18
[INFO] [stderr]     |
[INFO] [stderr] 109 |         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:109:34
[INFO] [stderr]     |
[INFO] [stderr] 109 |         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:156:32
[INFO] [stderr]     |
[INFO] [stderr] 156 |     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:156:46
[INFO] [stderr]     |
[INFO] [stderr] 156 |     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 102 warnings (run `cargo fix --bin "longcallR" -p longcallR --tests` to apply 34 suggestions)
[INFO] [stderr]     Finished `test` profile [unoptimized + debuginfo] target(s) in 0.19s
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/longcallR-728e424930e32cbb)
[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" "f0507c674910fff182d20f69f04331a70ecbd99a678bfa57d40637d9d67a0127", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "f0507c674910fff182d20f69f04331a70ecbd99a678bfa57d40637d9d67a0127", kill_on_drop: false }`
[INFO] [stdout] f0507c674910fff182d20f69f04331a70ecbd99a678bfa57d40637d9d67a0127
