[INFO] fetching crate longcallR 1.12.0... [INFO] building longcallR-1.12.0 against master#c7f6aa2869acdbf014d094c6e427e554e160b6db for pr-146237-2 [INFO] extracting crate longcallR 1.12.0 into /workspace/builds/worker-5-tc1/source [INFO] started tweaking crates.io crate longcallR 1.12.0 [INFO] finished tweaking crates.io crate longcallR 1.12.0 [INFO] tweaked toml for crates.io crate longcallR 1.12.0 written to /workspace/builds/worker-5-tc1/source/Cargo.toml [INFO] validating manifest of crates.io crate longcallR 1.12.0 on toolchain c7f6aa2869acdbf014d094c6e427e554e160b6db [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }` [INFO] crate crates.io crate longcallR 1.12.0 already has a lockfile, it will not be regenerated [INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }` [INFO] [stderr] Updating crates.io index [INFO] [stderr] Downloading crates ... [INFO] [stderr] Downloaded rust-htslib v0.46.0 [INFO] [stderr] Downloaded custom_derive v0.1.7 [INFO] [stderr] Downloaded itertools-num v0.1.3 [INFO] [stderr] Downloaded ndarray v0.15.6 [INFO] [stderr] Downloaded bio-types v1.0.4 [INFO] [stderr] Downloaded multimap v0.9.1 [INFO] [stderr] Downloaded special v0.10.3 [INFO] [stderr] Downloaded derive-new v0.6.0 [INFO] [stderr] Downloaded noodles-tabix v0.42.0 [INFO] [stderr] Downloaded fs-utils v1.1.4 [INFO] [stderr] Downloaded simba v0.6.0 [INFO] [stderr] Downloaded noodles-csi v0.36.0 [INFO] [stderr] Downloaded rust-lapper v1.2.0 [INFO] [stderr] Downloaded matrixmultiply v0.3.10 [INFO] [stderr] Downloaded nalgebra v0.29.0 [INFO] [stderr] Downloaded bio v1.6.0 [INFO] [stderr] Downloaded lambert_w v1.2.24 [INFO] [stderr] Downloaded noodles-core v0.15.0 [INFO] [stderr] Downloaded random v0.13.2 [INFO] [stderr] Downloaded thread-tree v0.3.3 [INFO] [stderr] Downloaded ieee754 v0.2.6 [INFO] [stderr] Downloaded rustc_version v0.1.7 [INFO] [stderr] Downloaded statrs v0.16.1 [INFO] [stderr] Downloaded editdistancek v1.0.2 [INFO] [stderr] Downloaded triple_accel v0.4.0 [INFO] [stderr] Downloaded linear-map v1.2.0 [INFO] [stderr] Downloaded probability v0.20.3 [INFO] [stderr] Downloaded newtype_derive v0.1.6 [INFO] [stderr] Downloaded noodles-bgzf v0.31.0 [INFO] [stderr] Downloaded hts-sys v2.2.0 [INFO] [stderr] Downloaded semver v0.1.20 [INFO] [stderr] Downloaded mathru v0.15.5 [INFO] [stderr] Downloaded noodles-vcf v0.60.0 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }` [INFO] [stdout] 61f909482ac7154aad1d96275f80e9492cba30b3c220913d6a59f3182a2d2697 [INFO] running `Command { std: "docker" "start" "-a" "61f909482ac7154aad1d96275f80e9492cba30b3c220913d6a59f3182a2d2697", kill_on_drop: false }` [INFO] running `Command { std: "docker" "inspect" "61f909482ac7154aad1d96275f80e9492cba30b3c220913d6a59f3182a2d2697", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "61f909482ac7154aad1d96275f80e9492cba30b3c220913d6a59f3182a2d2697", kill_on_drop: false }` [INFO] [stdout] 61f909482ac7154aad1d96275f80e9492cba30b3c220913d6a59f3182a2d2697 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "build" "--frozen" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 19baca08002c6c67296cca153b681cda9e2e08862fc035d2a86365d882a3a361 [INFO] running `Command { std: "docker" "start" "-a" "19baca08002c6c67296cca153b681cda9e2e08862fc035d2a86365d882a3a361", kill_on_drop: false }` [INFO] [stderr] Compiling matrixmultiply v0.3.10 [INFO] [stderr] Compiling semver v0.1.20 [INFO] [stderr] Compiling syn v2.0.104 [INFO] [stderr] Compiling jobserver v0.1.33 [INFO] [stderr] Compiling syn v1.0.109 [INFO] [stderr] Compiling bytemuck v1.23.2 [INFO] [stderr] Compiling num-complex v0.4.6 [INFO] [stderr] Compiling thread-tree v0.3.3 [INFO] [stderr] Compiling num-integer v0.1.46 [INFO] [stderr] Compiling quick-error v1.2.3 [INFO] [stderr] Compiling bit-vec v0.6.3 [INFO] [stderr] Compiling approx v0.5.1 [INFO] [stderr] Compiling bstr v1.12.0 [INFO] [stderr] Compiling glob v0.3.2 [INFO] [stderr] Compiling noodles-bgzf v0.31.0 [INFO] [stderr] Compiling rand_distr v0.4.3 [INFO] [stderr] Compiling fs-utils v1.1.4 [INFO] [stderr] Compiling anstyle v1.0.11 [INFO] [stderr] Compiling safe_arch v0.7.4 [INFO] [stderr] Compiling rustc_version v0.1.7 [INFO] [stderr] Compiling num-rational v0.4.2 [INFO] [stderr] Compiling lambert_w v1.2.24 [INFO] [stderr] Compiling cc v1.2.31 [INFO] [stderr] Compiling anstream v0.6.20 [INFO] [stderr] Compiling csv-core v0.1.12 [INFO] [stderr] Compiling custom_derive v0.1.7 [INFO] [stderr] Compiling petgraph v0.6.5 [INFO] [stderr] Compiling itertools v0.11.0 [INFO] [stderr] Compiling bit-set v0.5.3 [INFO] [stderr] Compiling itertools-num v0.1.3 [INFO] [stderr] Compiling special v0.10.3 [INFO] [stderr] Compiling wide v0.7.33 [INFO] [stderr] Compiling newtype_derive v0.1.6 [INFO] [stderr] Compiling ndarray v0.15.6 [INFO] [stderr] Compiling fxhash v0.2.1 [INFO] [stderr] Compiling triple_accel v0.4.0 [INFO] [stderr] Compiling noodles-core v0.15.0 [INFO] [stderr] Compiling ieee754 v0.2.6 [INFO] [stderr] Compiling clap_builder v4.5.43 [INFO] [stderr] Compiling strum v0.25.0 [INFO] [stderr] Compiling noodles-csi v0.36.0 [INFO] [stderr] Compiling linear-map v1.2.0 [INFO] [stderr] Compiling random v0.13.2 [INFO] [stderr] Compiling editdistancek v1.0.2 [INFO] [stderr] Compiling mathru v0.15.5 [INFO] [stderr] Compiling probability v0.20.3 [INFO] [stderr] Compiling cmake v0.1.54 [INFO] [stderr] Compiling noodles-tabix v0.42.0 [INFO] [stderr] Compiling noodles-vcf v0.60.0 [INFO] [stderr] Compiling libz-sys v1.1.22 [INFO] [stderr] Compiling hts-sys v2.2.0 [INFO] [stderr] Compiling simba v0.6.0 [INFO] [stderr] Compiling nalgebra-macros v0.1.0 [INFO] [stderr] Compiling derive-new v0.5.9 [INFO] [stderr] Compiling synstructure v0.13.2 [INFO] [stderr] Compiling zerofrom-derive v0.1.6 [INFO] [stderr] Compiling yoke-derive v0.8.0 [INFO] [stderr] Compiling zerovec-derive v0.11.1 [INFO] [stderr] Compiling displaydoc v0.2.5 [INFO] [stderr] Compiling serde_derive v1.0.219 [INFO] [stderr] Compiling thiserror-impl v1.0.69 [INFO] [stderr] Compiling strum_macros v0.26.4 [INFO] [stderr] Compiling derive-new v0.6.0 [INFO] [stderr] Compiling enum-map-derive v0.17.0 [INFO] [stderr] Compiling clap_derive v4.5.41 [INFO] [stderr] Compiling strum_macros v0.25.3 [INFO] [stderr] Compiling enum-map v2.7.3 [INFO] [stderr] Compiling thiserror v1.0.69 [INFO] [stderr] Compiling zerofrom v0.1.6 [INFO] [stderr] Compiling yoke v0.8.0 [INFO] [stderr] Compiling zerovec v0.11.4 [INFO] [stderr] Compiling zerotrie v0.2.2 [INFO] [stderr] Compiling bio-types v1.0.4 [INFO] [stderr] Compiling clap v4.5.43 [INFO] [stderr] Compiling tinystr v0.8.1 [INFO] [stderr] Compiling potential_utf v0.1.2 [INFO] [stderr] Compiling serde v1.0.219 [INFO] [stderr] Compiling icu_collections v2.0.0 [INFO] [stderr] Compiling icu_locale_core v2.0.0 [INFO] [stderr] Compiling icu_provider v2.0.0 [INFO] [stderr] Compiling icu_properties v2.0.1 [INFO] [stderr] Compiling icu_normalizer v2.0.0 [INFO] [stderr] Compiling nalgebra v0.29.0 [INFO] [stderr] Compiling idna_adapter v1.2.1 [INFO] [stderr] Compiling idna v1.0.3 [INFO] [stderr] Compiling url v2.5.4 [INFO] [stderr] Compiling bv v0.11.1 [INFO] [stderr] Compiling csv v1.3.1 [INFO] [stderr] Compiling multimap v0.9.1 [INFO] [stderr] Compiling vec_map v0.8.2 [INFO] [stderr] Compiling rust-lapper v1.2.0 [INFO] [stderr] Compiling rust-htslib v0.46.0 [INFO] [stderr] Compiling statrs v0.16.1 [INFO] [stderr] Compiling bio v1.6.0 [INFO] [stderr] Compiling longcallR v1.12.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `min` [INFO] [stdout] --> src/candidate.rs:2:16 [INFO] [stdout] | [INFO] [stdout] 2 | use std::cmp::{min, Ordering}; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashSet` [INFO] [stdout] --> src/candidate.rs:3:33 [INFO] [stdout] | [INFO] [stdout] 3 | use std::collections::{HashMap, HashSet}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Platform` [INFO] [stdout] --> src/candidate.rs:13:13 [INFO] [stdout] | [INFO] [stdout] 13 | use crate::{Platform, VALID_ALLELES}; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::exon::Exon` [INFO] [stdout] --> src/fragment.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::exon::Exon; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::hash::Hash` [INFO] [stdout] --> src/snp.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use std::hash::Hash; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `probability::distribution::Distribution` [INFO] [stdout] --> src/snp.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use probability::distribution::Distribution; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::exon::Exon` [INFO] [stdout] --> src/snp.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use crate::exon::Exon; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `LD_Pair` should have an upper camel case name [INFO] [stdout] --> src/snp.rs:93:12 [INFO] [stdout] | [INFO] [stdout] 93 | pub struct LD_Pair { [INFO] [stdout] | ^^^^^^^ help: convert the identifier to upper camel case: `LdPair` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` (part of `#[warn(nonstandard_style)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `itertools::Itertools` [INFO] [stdout] --> src/phase.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use itertools::Itertools; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `logprob` is never read [INFO] [stdout] --> src/candidate.rs:238:21 [INFO] [stdout] | [INFO] [stdout] 238 | let mut logprob = [0.0, 0.0, 0.0]; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:241:17 [INFO] [stdout] | [INFO] [stdout] 241 | let mut identical_baseqs; [INFO] [stdout] | ----^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:242:17 [INFO] [stdout] | [INFO] [stdout] 242 | let mut different_baseqs; [INFO] [stdout] | ----^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:324:17 [INFO] [stdout] | [INFO] [stdout] 324 | let mut genotype_prob = [ [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `snp1_ref_frac` is never read [INFO] [stdout] --> src/candidate.rs:638:26 [INFO] [stdout] | [INFO] [stdout] 638 | let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) = [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `snp1_alt_frac` is never read [INFO] [stdout] --> src/candidate.rs:638:45 [INFO] [stdout] | [INFO] [stdout] 638 | let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) = [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `snp2_ref_frac` is never read [INFO] [stdout] --> src/candidate.rs:638:64 [INFO] [stdout] | [INFO] [stdout] 638 | let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) = [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `snp2_alt_frac` is never read [INFO] [stdout] --> src/candidate.rs:638:83 [INFO] [stdout] | [INFO] [stdout] 638 | let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) = [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:637:22 [INFO] [stdout] | [INFO] [stdout] 637 | let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:637:36 [INFO] [stdout] | [INFO] [stdout] 637 | let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:637:50 [INFO] [stdout] | [INFO] [stdout] 637 | let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:637:64 [INFO] [stdout] | [INFO] [stdout] 637 | let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `snp_pos` is never read [INFO] [stdout] --> src/fragment.rs:61:21 [INFO] [stdout] | [INFO] [stdout] 61 | let mut snp_pos = -1; // pre-computed position of candidate SNPs [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ref_base` [INFO] [stdout] --> src/fragment.rs:101:33 [INFO] [stdout] | [INFO] [stdout] 101 | ... let ref_base = ref_seq[pos_on_ref as usize] as char; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_base` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `read_base` [INFO] [stdout] --> src/fragment.rs:102:33 [INFO] [stdout] | [INFO] [stdout] 102 | ... let read_base = seq[pos_on_query as usize] as char; [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_base` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `read_baseq` [INFO] [stdout] --> src/fragment.rs:103:33 [INFO] [stdout] | [INFO] [stdout] 103 | ... let read_baseq = record.qual()[pos_on_query as usize]; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] help: if this is intentional, prefix it with an underscore [INFO] [stdout] | [INFO] [stdout] 103 | let _read_baseq = record.qual()[pos_on_query as usize]; [INFO] [stdout] | + [INFO] [stdout] help: you might have meant to pattern match on the similarly named constant `MAX_BASE_QUALITY` [INFO] [stdout] | [INFO] [stdout] 103 - let read_baseq = record.qual()[pos_on_query as usize]; [INFO] [stdout] 103 + let constants::MAX_BASE_QUALITY = record.qual()[pos_on_query as usize]; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/fragment.rs:210:25 [INFO] [stdout] | [INFO] [stdout] 210 | let mut pair_start_idx: usize; [INFO] [stdout] | ----^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/fragment.rs:211:25 [INFO] [stdout] | [INFO] [stdout] 211 | let mut pair_end_idx: usize; [INFO] [stdout] | ----^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/fragment.rs:212:25 [INFO] [stdout] | [INFO] [stdout] 212 | let mut pair_start_base: u8; [INFO] [stdout] | ----^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/fragment.rs:213:25 [INFO] [stdout] | [INFO] [stdout] 213 | let mut pair_end_base: u8; [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/fragment.rs:318:25 [INFO] [stdout] | [INFO] [stdout] 318 | let mut frag = &mut self.fragments[frag_idx]; [INFO] [stdout] | ----^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/phase.rs:15:9 [INFO] [stdout] | [INFO] [stdout] 15 | let mut x: i32; [INFO] [stdout] | ----^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/phase.rs:38:9 [INFO] [stdout] | [INFO] [stdout] 38 | let mut x: i32; [INFO] [stdout] | ----^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `weight` is never read [INFO] [stdout] --> src/phase.rs:638:29 [INFO] [stdout] | [INFO] [stdout] 638 | let mut weight = 0; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `haplotype_genotype_increase` is never read [INFO] [stdout] --> src/phase.rs:867:17 [INFO] [stdout] | [INFO] [stdout] 867 | haplotype_genotype_increase = true; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `max_q` is never read [INFO] [stdout] --> src/phase.rs:923:29 [INFO] [stdout] | [INFO] [stdout] 923 | let mut max_q = 0.0; [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `q1` is never read [INFO] [stdout] --> src/phase.rs:1039:26 [INFO] [stdout] | [INFO] [stdout] 1039 | let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `q2` is never read [INFO] [stdout] --> src/phase.rs:1039:34 [INFO] [stdout] | [INFO] [stdout] 1039 | let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `q3` [INFO] [stdout] --> src/phase.rs:1039:42 [INFO] [stdout] | [INFO] [stdout] 1039 | let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_q3` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `q4` [INFO] [stdout] --> src/phase.rs:1039:50 [INFO] [stdout] | [INFO] [stdout] 1039 | let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_q4` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/phase.rs:1039:38 [INFO] [stdout] | [INFO] [stdout] 1039 | let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ----^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/phase.rs:1039:46 [INFO] [stdout] | [INFO] [stdout] 1039 | let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ----^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `pA` is never read [INFO] [stdout] --> src/snp.rs:111:18 [INFO] [stdout] | [INFO] [stdout] 111 | let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pa` is assigned to, but never used [INFO] [stdout] --> src/snp.rs:111:26 [INFO] [stdout] | [INFO] [stdout] 111 | let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_pa` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `pB` is never read [INFO] [stdout] --> src/snp.rs:111:34 [INFO] [stdout] | [INFO] [stdout] 111 | let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pb` is assigned to, but never used [INFO] [stdout] --> src/snp.rs:111:42 [INFO] [stdout] | [INFO] [stdout] 111 | let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_pb` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `pa` is never read [INFO] [stdout] --> src/snp.rs:141:9 [INFO] [stdout] | [INFO] [stdout] 141 | pa = aB + ab; // P(a) [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `pb` is never read [INFO] [stdout] --> src/snp.rs:143:9 [INFO] [stdout] | [INFO] [stdout] 143 | pb = Ab + ab; // P(b) [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/snp.rs:145:13 [INFO] [stdout] | [INFO] [stdout] 145 | let mut d = AB - pA * pB; // D= P(AB) - P(A)P(B) [INFO] [stdout] | ----^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `snp_pos` is never read [INFO] [stdout] --> src/snpfrags.rs:86:21 [INFO] [stdout] | [INFO] [stdout] 86 | let mut snp_pos = -1; // pre-computed position of candidate SNPs [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `alleles` is assigned to, but never used [INFO] [stdout] --> src/snpfrags.rs:87:21 [INFO] [stdout] | [INFO] [stdout] 87 | let mut alleles; // pre-computed alleles of candidate SNPs [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_alleles` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `alleles` is never read [INFO] [stdout] --> src/snpfrags.rs:90:17 [INFO] [stdout] | [INFO] [stdout] 90 | alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone(); [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `alleles` is never read [INFO] [stdout] --> src/snpfrags.rs:104:17 [INFO] [stdout] | [INFO] [stdout] 104 | alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone(); [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `alleles` is never read [INFO] [stdout] --> src/snpfrags.rs:141:37 [INFO] [stdout] | [INFO] [stdout] 141 | ... alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone(); [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `alleles` is never read [INFO] [stdout] --> src/snpfrags.rs:157:37 [INFO] [stdout] | [INFO] [stdout] 157 | ... alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone(); [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `alleles` is never read [INFO] [stdout] --> src/snpfrags.rs:169:37 [INFO] [stdout] | [INFO] [stdout] 169 | ... alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone(); [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score1` is never read [INFO] [stdout] --> src/snpfrags.rs:237:21 [INFO] [stdout] | [INFO] [stdout] 237 | let mut phase_score1 = 0.0; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score2` is never read [INFO] [stdout] --> src/snpfrags.rs:238:21 [INFO] [stdout] | [INFO] [stdout] 238 | let mut phase_score2 = 0.0; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score` is never read [INFO] [stdout] --> src/snpfrags.rs:239:21 [INFO] [stdout] | [INFO] [stdout] 239 | let mut phase_score = 0.0; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score1` is never read [INFO] [stdout] --> src/snpfrags.rs:329:21 [INFO] [stdout] | [INFO] [stdout] 329 | let mut phase_score1 = 0.0; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score2` is never read [INFO] [stdout] --> src/snpfrags.rs:330:21 [INFO] [stdout] | [INFO] [stdout] 330 | let mut phase_score2 = 0.0; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score` is never read [INFO] [stdout] --> src/snpfrags.rs:331:21 [INFO] [stdout] | [INFO] [stdout] 331 | let mut phase_score = 0.0; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `eta_i` [INFO] [stdout] --> src/snpfrags.rs:396:17 [INFO] [stdout] | [INFO] [stdout] 396 | let eta_i = snp.genotype; [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_eta_i` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score` is never read [INFO] [stdout] --> src/snpfrags.rs:480:21 [INFO] [stdout] | [INFO] [stdout] 480 | let mut phase_score = 0.0; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `q` is never read [INFO] [stdout] --> src/snpfrags.rs:577:25 [INFO] [stdout] | [INFO] [stdout] 577 | let mut q = 0.0; [INFO] [stdout] | ^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `qn` is never read [INFO] [stdout] --> src/snpfrags.rs:578:25 [INFO] [stdout] | [INFO] [stdout] 578 | let mut qn = 0.0; [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `region` [INFO] [stdout] --> src/snpfrags.rs:708:13 [INFO] [stdout] | [INFO] [stdout] 708 | let region = self.region.clone().to_string(); [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_region` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/somatic.rs:6:9 [INFO] [stdout] | [INFO] [stdout] 6 | let mut hap1_allele_class; [INFO] [stdout] | ----^^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/somatic.rs:7:9 [INFO] [stdout] | [INFO] [stdout] 7 | let mut hap2_allele_class; [INFO] [stdout] | ----^^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `cgi` [INFO] [stdout] --> src/util.rs:699:29 [INFO] [stdout] | [INFO] [stdout] 699 | for cgi in 0..cg.len() { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_cgi` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `gt` is never read [INFO] [stdout] --> src/vcf.rs:54:25 [INFO] [stdout] | [INFO] [stdout] 54 | let mut gt = "0/0"; [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `Exon` is never constructed [INFO] [stdout] --> src/exon.rs:4:12 [INFO] [stdout] | [INFO] [stdout] 4 | pub struct Exon { [INFO] [stdout] | ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `clean_fragments` is never used [INFO] [stdout] --> src/fragment.rs:311:12 [INFO] [stdout] | [INFO] [stdout] 9 | impl SNPFrag { [INFO] [stdout] | ------------ method in this implementation [INFO] [stdout] ... [INFO] [stdout] 311 | pub fn clean_fragments(&mut self) { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `qki` is never used [INFO] [stdout] --> src/phase.rs:14:8 [INFO] [stdout] | [INFO] [stdout] 14 | pub fn qki(sigma: i32, delta: i32, alt_fraction: f32, base_allele: i32, error_rate: f64) -> f64 { [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `cal_sigma_delta` is never used [INFO] [stdout] --> src/phase.rs:51:8 [INFO] [stdout] | [INFO] [stdout] 51 | pub fn cal_sigma_delta(sigma_k: i32, delta: &Vec, altfrac: &Vec, ps: &Vec, probs: &Vec) -> 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, ps: &Vec, probs: &Vec) -> 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, updated_haplotag: &HashMap src/phase.rs:401:8 [INFO] [stdout] | [INFO] [stdout] 401 | pub fn cal_inconsistent_percentage(delta_i: i32, sigma: &Vec, ps: &Vec) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_blocks` is never used [INFO] [stdout] --> src/phase.rs:411:8 [INFO] [stdout] | [INFO] [stdout] 411 | pub fn get_blocks(block_links: &HashMap<[usize; 2], i32>, weight_threshold: u32) -> (Vec>, GraphMap) { [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, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] 11 | pub hap1_alt_baseqs: Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] 12 | pub hap2_ref_baseqs: Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] 13 | pub hap2_alt_baseqs: Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `HapQuals` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `AlleleClass` is never constructed [INFO] [stdout] --> src/snp.rs:17:12 [INFO] [stdout] | [INFO] [stdout] 17 | pub struct AlleleClass { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `somatic`, `somatic_score`, and `hap_quals` are never read [INFO] [stdout] --> src/snp.rs:82:9 [INFO] [stdout] | [INFO] [stdout] 40 | pub struct CandidateSNP { [INFO] [stdout] | ------------ fields in this struct [INFO] [stdout] ... [INFO] [stdout] 82 | pub somatic: bool, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 83 | // detected somatic mutation by model [INFO] [stdout] 84 | pub somatic_score: f64, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] 85 | // phred somatic score [INFO] [stdout] 86 | pub hap_quals: HapQuals, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `CandidateSNP` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `calculate_LD_R2` is never used [INFO] [stdout] --> src/snp.rs:107:12 [INFO] [stdout] | [INFO] [stdout] 106 | impl LD_Pair { [INFO] [stdout] | ------------ method in this implementation [INFO] [stdout] 107 | pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `block_id` is never read [INFO] [stdout] --> src/snp.rs:243:9 [INFO] [stdout] | [INFO] [stdout] 242 | pub struct Block { [INFO] [stdout] | ----- field in this struct [INFO] [stdout] 243 | pub block_id: u32, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Block` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `phased` is never read [INFO] [stdout] --> src/snpfrags.rs:29:9 [INFO] [stdout] | [INFO] [stdout] 15 | pub struct SNPFrag { [INFO] [stdout] | ------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 29 | pub phased: bool, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `SNPFrag` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `get_somatic_haplotype_baseqs` and `detect_somatic_by_het` are never used [INFO] [stdout] --> src/snpfrags.rs:56:12 [INFO] [stdout] | [INFO] [stdout] 55 | impl SNPFrag { [INFO] [stdout] | ------------ methods in this implementation [INFO] [stdout] 56 | pub fn get_somatic_haplotype_baseqs(&mut self, bam_path: &str, region: &Region, phased_fragments: &HashMap) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 735 | pub fn detect_somatic_by_het(&mut self, bam_path: &str, region: &Region) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_prob_somatic` is never used [INFO] [stdout] --> src/somatic.rs:5:8 [INFO] [stdout] | [INFO] [stdout] 5 | pub fn calculate_prob_somatic(hap1_ref_baseqs: &Vec, hap1_alt_baseqs: &Vec, hap2_ref_baseqs: &Vec, hap2_alt_baseqs: &Vec,... [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `get_main_alleles` and `get_none_ref_count` are never used [INFO] [stdout] --> src/util.rs:178:12 [INFO] [stdout] | [INFO] [stdout] 129 | impl BaseFreq { [INFO] [stdout] | ------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 178 | pub fn get_main_alleles(&self) -> Vec<(char, u32)> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 203 | pub fn get_none_ref_count(&self) -> u32 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_vcf` is never used [INFO] [stdout] --> src/vcf.rs:309:8 [INFO] [stdout] | [INFO] [stdout] 309 | pub fn load_vcf( [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `phased` is never read [INFO] [stdout] --> src/vcf.rs:397:9 [INFO] [stdout] | [INFO] [stdout] 394 | pub struct GenotypeAndQuality { [INFO] [stdout] | ------------------ field in this struct [INFO] [stdout] ... [INFO] [stdout] 397 | pub phased: bool, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `GenotypeAndQuality` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `init_haplotypes_LD2` should have a snake case name [INFO] [stdout] --> src/phase.rs:609:19 [INFO] [stdout] | [INFO] [stdout] 609 | pub unsafe fn init_haplotypes_LD2(&mut self, ld_graph: &GraphMap, ld_weight_threshold: u32) -> HashSet { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `init_haplotypes_ld2` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `calculate_LD_R2` should have a snake case name [INFO] [stdout] --> src/snp.rs:107:12 [INFO] [stdout] | [INFO] [stdout] 107 | pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 { [INFO] [stdout] | ^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `calculate_ld_r2` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `A` should have a snake case name [INFO] [stdout] --> src/snp.rs:107:35 [INFO] [stdout] | [INFO] [stdout] 107 | pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 { [INFO] [stdout] | ^ help: convert the identifier to snake case: `a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `B` should have a snake case name [INFO] [stdout] --> src/snp.rs:107:49 [INFO] [stdout] | [INFO] [stdout] 107 | pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 { [INFO] [stdout] | ^ help: convert the identifier to snake case: `b` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `AB` should have a snake case name [INFO] [stdout] --> src/snp.rs:110:18 [INFO] [stdout] | [INFO] [stdout] 110 | let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: convert the identifier to snake case: `ab` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `Ab` should have a snake case name [INFO] [stdout] --> src/snp.rs:110:26 [INFO] [stdout] | [INFO] [stdout] 110 | let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: convert the identifier to snake case: `ab` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `aB` should have a snake case name [INFO] [stdout] --> src/snp.rs:110:34 [INFO] [stdout] | [INFO] [stdout] 110 | let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: convert the identifier to snake case: `a_b` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pA` should have a snake case name [INFO] [stdout] --> src/snp.rs:111:18 [INFO] [stdout] | [INFO] [stdout] 111 | let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pB` should have a snake case name [INFO] [stdout] --> src/snp.rs:111:34 [INFO] [stdout] | [INFO] [stdout] 111 | let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_b` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `A` should have a snake case name [INFO] [stdout] --> src/snp.rs:158:32 [INFO] [stdout] | [INFO] [stdout] 158 | pub fn calculate_ld(&self, A: u8, a: u8, B: u8, b: u8) -> (f32, i32) { [INFO] [stdout] | ^ help: convert the identifier to snake case: `a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `B` should have a snake case name [INFO] [stdout] --> src/snp.rs:158:46 [INFO] [stdout] | [INFO] [stdout] 158 | pub fn calculate_ld(&self, A: u8, a: u8, B: u8, b: u8) -> (f32, i32) { [INFO] [stdout] | ^ help: convert the identifier to snake case: `b` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 07s [INFO] running `Command { std: "docker" "inspect" "19baca08002c6c67296cca153b681cda9e2e08862fc035d2a86365d882a3a361", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "19baca08002c6c67296cca153b681cda9e2e08862fc035d2a86365d882a3a361", kill_on_drop: false }` [INFO] [stdout] 19baca08002c6c67296cca153b681cda9e2e08862fc035d2a86365d882a3a361 [INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-5-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:e90291280db7d1fac5b66fc6dad9f9662629e7365a55743daf9bdf73ebc4ea79" "/opt/rustwide/cargo-home/bin/cargo" "+c7f6aa2869acdbf014d094c6e427e554e160b6db" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }` [INFO] [stdout] 53ff017707b88bf68ebfdfd07dbacdd657f0e2a721587b8d96b19a24c06e5ef2 [INFO] running `Command { std: "docker" "start" "-a" "53ff017707b88bf68ebfdfd07dbacdd657f0e2a721587b8d96b19a24c06e5ef2", kill_on_drop: false }` [INFO] [stderr] Compiling longcallR v1.12.0 (/opt/rustwide/workdir) [INFO] [stdout] warning: unused import: `min` [INFO] [stdout] --> src/candidate.rs:2:16 [INFO] [stdout] | [INFO] [stdout] 2 | use std::cmp::{min, Ordering}; [INFO] [stdout] | ^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `HashSet` [INFO] [stdout] --> src/candidate.rs:3:33 [INFO] [stdout] | [INFO] [stdout] 3 | use std::collections::{HashMap, HashSet}; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `Platform` [INFO] [stdout] --> src/candidate.rs:13:13 [INFO] [stdout] | [INFO] [stdout] 13 | use crate::{Platform, VALID_ALLELES}; [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::exon::Exon` [INFO] [stdout] --> src/fragment.rs:1:5 [INFO] [stdout] | [INFO] [stdout] 1 | use crate::exon::Exon; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `std::hash::Hash` [INFO] [stdout] --> src/snp.rs:2:5 [INFO] [stdout] | [INFO] [stdout] 2 | use std::hash::Hash; [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `probability::distribution::Distribution` [INFO] [stdout] --> src/snp.rs:4:5 [INFO] [stdout] | [INFO] [stdout] 4 | use probability::distribution::Distribution; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `crate::exon::Exon` [INFO] [stdout] --> src/snp.rs:6:5 [INFO] [stdout] | [INFO] [stdout] 6 | use crate::exon::Exon; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: type `LD_Pair` should have an upper camel case name [INFO] [stdout] --> src/snp.rs:93:12 [INFO] [stdout] | [INFO] [stdout] 93 | pub struct LD_Pair { [INFO] [stdout] | ^^^^^^^ help: convert the identifier to upper camel case: `LdPair` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_camel_case_types)]` (part of `#[warn(nonstandard_style)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused import: `itertools::Itertools` [INFO] [stdout] --> src/phase.rs:3:5 [INFO] [stdout] | [INFO] [stdout] 3 | use itertools::Itertools; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `logprob` is never read [INFO] [stdout] --> src/candidate.rs:238:21 [INFO] [stdout] | [INFO] [stdout] 238 | let mut logprob = [0.0, 0.0, 0.0]; [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:241:17 [INFO] [stdout] | [INFO] [stdout] 241 | let mut identical_baseqs; [INFO] [stdout] | ----^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:242:17 [INFO] [stdout] | [INFO] [stdout] 242 | let mut different_baseqs; [INFO] [stdout] | ----^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:324:17 [INFO] [stdout] | [INFO] [stdout] 324 | let mut genotype_prob = [ [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `snp1_ref_frac` is never read [INFO] [stdout] --> src/candidate.rs:638:26 [INFO] [stdout] | [INFO] [stdout] 638 | let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) = [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `snp1_alt_frac` is never read [INFO] [stdout] --> src/candidate.rs:638:45 [INFO] [stdout] | [INFO] [stdout] 638 | let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) = [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `snp2_ref_frac` is never read [INFO] [stdout] --> src/candidate.rs:638:64 [INFO] [stdout] | [INFO] [stdout] 638 | let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) = [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `snp2_alt_frac` is never read [INFO] [stdout] --> src/candidate.rs:638:83 [INFO] [stdout] | [INFO] [stdout] 638 | let (mut snp1_ref_frac, mut snp1_alt_frac, mut snp2_ref_frac, mut snp2_alt_frac) = [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:637:22 [INFO] [stdout] | [INFO] [stdout] 637 | let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:637:36 [INFO] [stdout] | [INFO] [stdout] 637 | let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:637:50 [INFO] [stdout] | [INFO] [stdout] 637 | let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/candidate.rs:637:64 [INFO] [stdout] | [INFO] [stdout] 637 | let (mut snp1_ref, mut snp1_alt, mut snp2_ref, mut snp2_alt); [INFO] [stdout] | ----^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `snp_pos` is never read [INFO] [stdout] --> src/fragment.rs:61:21 [INFO] [stdout] | [INFO] [stdout] 61 | let mut snp_pos = -1; // pre-computed position of candidate SNPs [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `ref_base` [INFO] [stdout] --> src/fragment.rs:101:33 [INFO] [stdout] | [INFO] [stdout] 101 | ... let ref_base = ref_seq[pos_on_ref as usize] as char; [INFO] [stdout] | ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_ref_base` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `read_base` [INFO] [stdout] --> src/fragment.rs:102:33 [INFO] [stdout] | [INFO] [stdout] 102 | ... let read_base = seq[pos_on_query as usize] as char; [INFO] [stdout] | ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_read_base` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `read_baseq` [INFO] [stdout] --> src/fragment.rs:103:33 [INFO] [stdout] | [INFO] [stdout] 103 | ... let read_baseq = record.qual()[pos_on_query as usize]; [INFO] [stdout] | ^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] help: if this is intentional, prefix it with an underscore [INFO] [stdout] | [INFO] [stdout] 103 | let _read_baseq = record.qual()[pos_on_query as usize]; [INFO] [stdout] | + [INFO] [stdout] help: you might have meant to pattern match on the similarly named constant `MAX_BASE_QUALITY` [INFO] [stdout] | [INFO] [stdout] 103 - let read_baseq = record.qual()[pos_on_query as usize]; [INFO] [stdout] 103 + let constants::MAX_BASE_QUALITY = record.qual()[pos_on_query as usize]; [INFO] [stdout] | [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/fragment.rs:210:25 [INFO] [stdout] | [INFO] [stdout] 210 | let mut pair_start_idx: usize; [INFO] [stdout] | ----^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/fragment.rs:211:25 [INFO] [stdout] | [INFO] [stdout] 211 | let mut pair_end_idx: usize; [INFO] [stdout] | ----^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/fragment.rs:212:25 [INFO] [stdout] | [INFO] [stdout] 212 | let mut pair_start_base: u8; [INFO] [stdout] | ----^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/fragment.rs:213:25 [INFO] [stdout] | [INFO] [stdout] 213 | let mut pair_end_base: u8; [INFO] [stdout] | ----^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/fragment.rs:318:25 [INFO] [stdout] | [INFO] [stdout] 318 | let mut frag = &mut self.fragments[frag_idx]; [INFO] [stdout] | ----^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/phase.rs:15:9 [INFO] [stdout] | [INFO] [stdout] 15 | let mut x: i32; [INFO] [stdout] | ----^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/phase.rs:38:9 [INFO] [stdout] | [INFO] [stdout] 38 | let mut x: i32; [INFO] [stdout] | ----^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `weight` is never read [INFO] [stdout] --> src/phase.rs:638:29 [INFO] [stdout] | [INFO] [stdout] 638 | let mut weight = 0; [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `haplotype_genotype_increase` is never read [INFO] [stdout] --> src/phase.rs:867:17 [INFO] [stdout] | [INFO] [stdout] 867 | haplotype_genotype_increase = true; [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `max_q` is never read [INFO] [stdout] --> src/phase.rs:923:29 [INFO] [stdout] | [INFO] [stdout] 923 | let mut max_q = 0.0; [INFO] [stdout] | ^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `q1` is never read [INFO] [stdout] --> src/phase.rs:1039:26 [INFO] [stdout] | [INFO] [stdout] 1039 | let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `q2` is never read [INFO] [stdout] --> src/phase.rs:1039:34 [INFO] [stdout] | [INFO] [stdout] 1039 | let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `q3` [INFO] [stdout] --> src/phase.rs:1039:42 [INFO] [stdout] | [INFO] [stdout] 1039 | let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_q3` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `q4` [INFO] [stdout] --> src/phase.rs:1039:50 [INFO] [stdout] | [INFO] [stdout] 1039 | let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: if this is intentional, prefix it with an underscore: `_q4` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/phase.rs:1039:38 [INFO] [stdout] | [INFO] [stdout] 1039 | let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ----^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/phase.rs:1039:46 [INFO] [stdout] | [INFO] [stdout] 1039 | let (mut q1, mut q2, mut q3, mut q4) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ----^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `pA` is never read [INFO] [stdout] --> src/snp.rs:111:18 [INFO] [stdout] | [INFO] [stdout] 111 | let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pa` is assigned to, but never used [INFO] [stdout] --> src/snp.rs:111:26 [INFO] [stdout] | [INFO] [stdout] 111 | let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_pa` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `pB` is never read [INFO] [stdout] --> src/snp.rs:111:34 [INFO] [stdout] | [INFO] [stdout] 111 | let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pb` is assigned to, but never used [INFO] [stdout] --> src/snp.rs:111:42 [INFO] [stdout] | [INFO] [stdout] 111 | let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_pb` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `pa` is never read [INFO] [stdout] --> src/snp.rs:141:9 [INFO] [stdout] | [INFO] [stdout] 141 | pa = aB + ab; // P(a) [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `pb` is never read [INFO] [stdout] --> src/snp.rs:143:9 [INFO] [stdout] | [INFO] [stdout] 143 | pb = Ab + ab; // P(b) [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/snp.rs:145:13 [INFO] [stdout] | [INFO] [stdout] 145 | let mut d = AB - pA * pB; // D= P(AB) - P(A)P(B) [INFO] [stdout] | ----^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `snp_pos` is never read [INFO] [stdout] --> src/snpfrags.rs:86:21 [INFO] [stdout] | [INFO] [stdout] 86 | let mut snp_pos = -1; // pre-computed position of candidate SNPs [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `alleles` is assigned to, but never used [INFO] [stdout] --> src/snpfrags.rs:87:21 [INFO] [stdout] | [INFO] [stdout] 87 | let mut alleles; // pre-computed alleles of candidate SNPs [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: consider using `_alleles` instead [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `alleles` is never read [INFO] [stdout] --> src/snpfrags.rs:90:17 [INFO] [stdout] | [INFO] [stdout] 90 | alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone(); [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `alleles` is never read [INFO] [stdout] --> src/snpfrags.rs:104:17 [INFO] [stdout] | [INFO] [stdout] 104 | alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone(); [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `alleles` is never read [INFO] [stdout] --> src/snpfrags.rs:141:37 [INFO] [stdout] | [INFO] [stdout] 141 | ... alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone(); [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `alleles` is never read [INFO] [stdout] --> src/snpfrags.rs:157:37 [INFO] [stdout] | [INFO] [stdout] 157 | ... alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone(); [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `alleles` is never read [INFO] [stdout] --> src/snpfrags.rs:169:37 [INFO] [stdout] | [INFO] [stdout] 169 | ... alleles = self.candidate_snps[self.somatic_snps[idx]].alleles.clone(); [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score1` is never read [INFO] [stdout] --> src/snpfrags.rs:237:21 [INFO] [stdout] | [INFO] [stdout] 237 | let mut phase_score1 = 0.0; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score2` is never read [INFO] [stdout] --> src/snpfrags.rs:238:21 [INFO] [stdout] | [INFO] [stdout] 238 | let mut phase_score2 = 0.0; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score` is never read [INFO] [stdout] --> src/snpfrags.rs:239:21 [INFO] [stdout] | [INFO] [stdout] 239 | let mut phase_score = 0.0; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score1` is never read [INFO] [stdout] --> src/snpfrags.rs:329:21 [INFO] [stdout] | [INFO] [stdout] 329 | let mut phase_score1 = 0.0; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score2` is never read [INFO] [stdout] --> src/snpfrags.rs:330:21 [INFO] [stdout] | [INFO] [stdout] 330 | let mut phase_score2 = 0.0; [INFO] [stdout] | ^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score` is never read [INFO] [stdout] --> src/snpfrags.rs:331:21 [INFO] [stdout] | [INFO] [stdout] 331 | let mut phase_score = 0.0; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `eta_i` [INFO] [stdout] --> src/snpfrags.rs:396:17 [INFO] [stdout] | [INFO] [stdout] 396 | let eta_i = snp.genotype; [INFO] [stdout] | ^^^^^ help: if this is intentional, prefix it with an underscore: `_eta_i` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `phase_score` is never read [INFO] [stdout] --> src/snpfrags.rs:480:21 [INFO] [stdout] | [INFO] [stdout] 480 | let mut phase_score = 0.0; [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `q` is never read [INFO] [stdout] --> src/snpfrags.rs:577:25 [INFO] [stdout] | [INFO] [stdout] 577 | let mut q = 0.0; [INFO] [stdout] | ^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `qn` is never read [INFO] [stdout] --> src/snpfrags.rs:578:25 [INFO] [stdout] | [INFO] [stdout] 578 | let mut qn = 0.0; [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `region` [INFO] [stdout] --> src/snpfrags.rs:708:13 [INFO] [stdout] | [INFO] [stdout] 708 | let region = self.region.clone().to_string(); [INFO] [stdout] | ^^^^^^ help: if this is intentional, prefix it with an underscore: `_region` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/somatic.rs:6:9 [INFO] [stdout] | [INFO] [stdout] 6 | let mut hap1_allele_class; [INFO] [stdout] | ----^^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable does not need to be mutable [INFO] [stdout] --> src/somatic.rs:7:9 [INFO] [stdout] | [INFO] [stdout] 7 | let mut hap2_allele_class; [INFO] [stdout] | ----^^^^^^^^^^^^^^^^^ [INFO] [stdout] | | [INFO] [stdout] | help: remove this `mut` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: unused variable: `cgi` [INFO] [stdout] --> src/util.rs:699:29 [INFO] [stdout] | [INFO] [stdout] 699 | for cgi in 0..cg.len() { [INFO] [stdout] | ^^^ help: if this is intentional, prefix it with an underscore: `_cgi` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: value assigned to `gt` is never read [INFO] [stdout] --> src/vcf.rs:54:25 [INFO] [stdout] | [INFO] [stdout] 54 | let mut gt = "0/0"; [INFO] [stdout] | ^^ [INFO] [stdout] | [INFO] [stdout] = help: maybe it is overwritten before being read? [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `Exon` is never constructed [INFO] [stdout] --> src/exon.rs:4:12 [INFO] [stdout] | [INFO] [stdout] 4 | pub struct Exon { [INFO] [stdout] | ^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `clean_fragments` is never used [INFO] [stdout] --> src/fragment.rs:311:12 [INFO] [stdout] | [INFO] [stdout] 9 | impl SNPFrag { [INFO] [stdout] | ------------ method in this implementation [INFO] [stdout] ... [INFO] [stdout] 311 | pub fn clean_fragments(&mut self) { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `qki` is never used [INFO] [stdout] --> src/phase.rs:14:8 [INFO] [stdout] | [INFO] [stdout] 14 | pub fn qki(sigma: i32, delta: i32, alt_fraction: f32, base_allele: i32, error_rate: f64) -> f64 { [INFO] [stdout] | ^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `cal_sigma_delta` is never used [INFO] [stdout] --> src/phase.rs:51:8 [INFO] [stdout] | [INFO] [stdout] 51 | pub fn cal_sigma_delta(sigma_k: i32, delta: &Vec, altfrac: &Vec, ps: &Vec, probs: &Vec) -> 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, ps: &Vec, probs: &Vec) -> 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, updated_haplotag: &HashMap src/phase.rs:401:8 [INFO] [stdout] | [INFO] [stdout] 401 | pub fn cal_inconsistent_percentage(delta_i: i32, sigma: &Vec, ps: &Vec) -> f64 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `get_blocks` is never used [INFO] [stdout] --> src/phase.rs:411:8 [INFO] [stdout] | [INFO] [stdout] 411 | pub fn get_blocks(block_links: &HashMap<[usize; 2], i32>, weight_threshold: u32) -> (Vec>, GraphMap) { [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, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] 11 | pub hap1_alt_baseqs: Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] 12 | pub hap2_ref_baseqs: Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] 13 | pub hap2_alt_baseqs: Vec, [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `HapQuals` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: struct `AlleleClass` is never constructed [INFO] [stdout] --> src/snp.rs:17:12 [INFO] [stdout] | [INFO] [stdout] 17 | pub struct AlleleClass { [INFO] [stdout] | ^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: fields `somatic`, `somatic_score`, and `hap_quals` are never read [INFO] [stdout] --> src/snp.rs:82:9 [INFO] [stdout] | [INFO] [stdout] 40 | pub struct CandidateSNP { [INFO] [stdout] | ------------ fields in this struct [INFO] [stdout] ... [INFO] [stdout] 82 | pub somatic: bool, [INFO] [stdout] | ^^^^^^^ [INFO] [stdout] 83 | // detected somatic mutation by model [INFO] [stdout] 84 | pub somatic_score: f64, [INFO] [stdout] | ^^^^^^^^^^^^^ [INFO] [stdout] 85 | // phred somatic score [INFO] [stdout] 86 | pub hap_quals: HapQuals, [INFO] [stdout] | ^^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `CandidateSNP` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `calculate_LD_R2` is never used [INFO] [stdout] --> src/snp.rs:107:12 [INFO] [stdout] | [INFO] [stdout] 106 | impl LD_Pair { [INFO] [stdout] | ------------ method in this implementation [INFO] [stdout] 107 | pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 { [INFO] [stdout] | ^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `block_id` is never read [INFO] [stdout] --> src/snp.rs:243:9 [INFO] [stdout] | [INFO] [stdout] 242 | pub struct Block { [INFO] [stdout] | ----- field in this struct [INFO] [stdout] 243 | pub block_id: u32, [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `Block` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `phased` is never read [INFO] [stdout] --> src/snpfrags.rs:29:9 [INFO] [stdout] | [INFO] [stdout] 15 | pub struct SNPFrag { [INFO] [stdout] | ------- field in this struct [INFO] [stdout] ... [INFO] [stdout] 29 | pub phased: bool, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `SNPFrag` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `get_somatic_haplotype_baseqs` and `detect_somatic_by_het` are never used [INFO] [stdout] --> src/snpfrags.rs:56:12 [INFO] [stdout] | [INFO] [stdout] 55 | impl SNPFrag { [INFO] [stdout] | ------------ methods in this implementation [INFO] [stdout] 56 | pub fn get_somatic_haplotype_baseqs(&mut self, bam_path: &str, region: &Region, phased_fragments: &HashMap) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 735 | pub fn detect_somatic_by_het(&mut self, bam_path: &str, region: &Region) { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `calculate_prob_somatic` is never used [INFO] [stdout] --> src/somatic.rs:5:8 [INFO] [stdout] | [INFO] [stdout] 5 | pub fn calculate_prob_somatic(hap1_ref_baseqs: &Vec, hap1_alt_baseqs: &Vec, hap2_ref_baseqs: &Vec, hap2_alt_baseqs: &Vec,... [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: methods `get_main_alleles` and `get_none_ref_count` are never used [INFO] [stdout] --> src/util.rs:178:12 [INFO] [stdout] | [INFO] [stdout] 129 | impl BaseFreq { [INFO] [stdout] | ------------- methods in this implementation [INFO] [stdout] ... [INFO] [stdout] 178 | pub fn get_main_alleles(&self) -> Vec<(char, u32)> { [INFO] [stdout] | ^^^^^^^^^^^^^^^^ [INFO] [stdout] ... [INFO] [stdout] 203 | pub fn get_none_ref_count(&self) -> u32 { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: function `load_vcf` is never used [INFO] [stdout] --> src/vcf.rs:309:8 [INFO] [stdout] | [INFO] [stdout] 309 | pub fn load_vcf( [INFO] [stdout] | ^^^^^^^^ [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: field `phased` is never read [INFO] [stdout] --> src/vcf.rs:397:9 [INFO] [stdout] | [INFO] [stdout] 394 | pub struct GenotypeAndQuality { [INFO] [stdout] | ------------------ field in this struct [INFO] [stdout] ... [INFO] [stdout] 397 | pub phased: bool, [INFO] [stdout] | ^^^^^^ [INFO] [stdout] | [INFO] [stdout] = note: `GenotypeAndQuality` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `init_haplotypes_LD2` should have a snake case name [INFO] [stdout] --> src/phase.rs:609:19 [INFO] [stdout] | [INFO] [stdout] 609 | pub unsafe fn init_haplotypes_LD2(&mut self, ld_graph: &GraphMap, ld_weight_threshold: u32) -> HashSet { [INFO] [stdout] | ^^^^^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `init_haplotypes_ld2` [INFO] [stdout] | [INFO] [stdout] = note: `#[warn(non_snake_case)]` (part of `#[warn(nonstandard_style)]`) on by default [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: method `calculate_LD_R2` should have a snake case name [INFO] [stdout] --> src/snp.rs:107:12 [INFO] [stdout] | [INFO] [stdout] 107 | pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 { [INFO] [stdout] | ^^^^^^^^^^^^^^^ help: convert the identifier to snake case: `calculate_ld_r2` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `A` should have a snake case name [INFO] [stdout] --> src/snp.rs:107:35 [INFO] [stdout] | [INFO] [stdout] 107 | pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 { [INFO] [stdout] | ^ help: convert the identifier to snake case: `a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `B` should have a snake case name [INFO] [stdout] --> src/snp.rs:107:49 [INFO] [stdout] | [INFO] [stdout] 107 | pub fn calculate_LD_R2(&self, A: u8, a: u8, B: u8, b: u8) -> f32 { [INFO] [stdout] | ^ help: convert the identifier to snake case: `b` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `AB` should have a snake case name [INFO] [stdout] --> src/snp.rs:110:18 [INFO] [stdout] | [INFO] [stdout] 110 | let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: convert the identifier to snake case: `ab` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `Ab` should have a snake case name [INFO] [stdout] --> src/snp.rs:110:26 [INFO] [stdout] | [INFO] [stdout] 110 | let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: convert the identifier to snake case: `ab` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `aB` should have a snake case name [INFO] [stdout] --> src/snp.rs:110:34 [INFO] [stdout] | [INFO] [stdout] 110 | let (mut AB, mut Ab, mut aB, mut ab, mut sum) = (0.0, 0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: convert the identifier to snake case: `a_b` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pA` should have a snake case name [INFO] [stdout] --> src/snp.rs:111:18 [INFO] [stdout] | [INFO] [stdout] 111 | let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `pB` should have a snake case name [INFO] [stdout] --> src/snp.rs:111:34 [INFO] [stdout] | [INFO] [stdout] 111 | let (mut pA, mut pa, mut pB, mut pb) = (0.0, 0.0, 0.0, 0.0); [INFO] [stdout] | ^^ help: convert the identifier to snake case: `p_b` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `A` should have a snake case name [INFO] [stdout] --> src/snp.rs:158:32 [INFO] [stdout] | [INFO] [stdout] 158 | pub fn calculate_ld(&self, A: u8, a: u8, B: u8, b: u8) -> (f32, i32) { [INFO] [stdout] | ^ help: convert the identifier to snake case: `a` [INFO] [stdout] [INFO] [stdout] [INFO] [stdout] warning: variable `B` should have a snake case name [INFO] [stdout] --> src/snp.rs:158:46 [INFO] [stdout] | [INFO] [stdout] 158 | pub fn calculate_ld(&self, A: u8, a: u8, B: u8, b: u8) -> (f32, i32) { [INFO] [stdout] | ^ help: convert the identifier to snake case: `b` [INFO] [stdout] [INFO] [stdout] [INFO] [stderr] Finished `test` profile [unoptimized + debuginfo] target(s) in 1.83s [INFO] running `Command { std: "docker" "inspect" "53ff017707b88bf68ebfdfd07dbacdd657f0e2a721587b8d96b19a24c06e5ef2", kill_on_drop: false }` [INFO] running `Command { std: "docker" "rm" "-f" "53ff017707b88bf68ebfdfd07dbacdd657f0e2a721587b8d96b19a24c06e5ef2", kill_on_drop: false }` [INFO] [stdout] 53ff017707b88bf68ebfdfd07dbacdd657f0e2a721587b8d96b19a24c06e5ef2