[INFO] cloning repository https://github.com/keithyin/aligned_bam_stat
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/keithyin/aligned_bam_stat" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Faligned_bam_stat", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Faligned_bam_stat'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 9c2436638b62703967cadf74ba6ffbe419e4e166
[INFO] checking keithyin/aligned_bam_stat against 1.95.0 for pr-155915
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fkeithyin%2Faligned_bam_stat" "/workspace/builds/worker-4-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-4-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/keithyin/aligned_bam_stat
[INFO] finished tweaking git repo https://github.com/keithyin/aligned_bam_stat
[INFO] tweaked toml for git repo https://github.com/keithyin/aligned_bam_stat written to /workspace/builds/worker-4-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/keithyin/aligned_bam_stat on toolchain 1.95.0
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+1.95.0" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/keithyin/aligned_bam_stat 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" "+1.95.0" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
[INFO] [stderr]     Updating crates.io index
[INFO] [stderr]  Downloading crates ...
[INFO] [stderr]   Downloaded ieee754 v0.2.6
[INFO] [stderr]   Downloaded fs-utils v1.1.4
[INFO] [stderr]   Downloaded itertools-num v0.1.3
[INFO] [stderr]   Downloaded derive-new v0.6.0
[INFO] [stderr]   Downloaded newtype_derive v0.1.6
[INFO] [stderr]   Downloaded foreign_vec v0.1.0
[INFO] [stderr]   Downloaded multiversion v0.7.4
[INFO] [stderr]   Downloaded multiversion-macros v0.7.4
[INFO] [stderr]   Downloaded editdistancek v1.0.2
[INFO] [stderr]   Downloaded now v0.1.3
[INFO] [stderr]   Downloaded lz4 v1.28.1
[INFO] [stderr]   Downloaded polars-row v0.36.2
[INFO] [stderr]   Downloaded array-init-cursor v0.2.1
[INFO] [stderr]   Downloaded multimap v0.9.1
[INFO] [stderr]   Downloaded polars-compute v0.36.2
[INFO] [stderr]   Downloaded openssl-sys v0.9.114
[INFO] [stderr]   Downloaded ordered-float v3.9.2
[INFO] [stderr]   Downloaded polars-sql v0.36.2
[INFO] [stderr]   Downloaded bio-types v1.0.4
[INFO] [stderr]   Downloaded atoi_simd v0.15.6
[INFO] [stderr]   Downloaded triple_accel v0.4.0
[INFO] [stderr]   Downloaded arrow-format v0.8.1
[INFO] [stderr]   Downloaded enum_dispatch v0.3.13
[INFO] [stderr]   Downloaded simba v0.6.0
[INFO] [stderr]   Downloaded ethnum v1.5.3
[INFO] [stderr]   Downloaded bam v0.1.4
[INFO] [stderr]   Downloaded polars-io v0.36.2
[INFO] [stderr]   Downloaded polars-pipe v0.36.2
[INFO] [stderr]   Downloaded argminmax v0.6.3
[INFO] [stderr]   Downloaded polars-lazy v0.36.2
[INFO] [stderr]   Downloaded polars-ops v0.36.2
[INFO] [stderr]   Downloaded sqlparser v0.39.0
[INFO] [stderr]   Downloaded statrs v0.16.1
[INFO] [stderr]   Downloaded bio v1.6.0
[INFO] [stderr]   Downloaded polars-plan v0.36.2
[INFO] [stderr]   Downloaded polars v0.36.2
[INFO] [stderr]   Downloaded polars-time v0.36.2
[INFO] [stderr]   Downloaded rust-htslib v0.47.1
[INFO] [stderr]   Downloaded target-features v0.1.6
[INFO] [stderr]   Downloaded polars-arrow v0.36.2
[INFO] [stderr]   Downloaded planus v0.3.1
[INFO] [stderr]   Downloaded nalgebra v0.29.0
[INFO] [stderr]   Downloaded polars-core v0.36.2
[INFO] [stderr]   Downloaded lz4-sys v1.11.1+lz4-1.10.0
[INFO] [stderr]   Downloaded polars-utils v0.36.2
[INFO] [stderr]   Downloaded smartstring v1.0.1
[INFO] [stderr]   Downloaded polars-error v0.36.2
[INFO] [stderr]   Downloaded libz-sys v1.1.28
[INFO] [stderr]   Downloaded curl-sys v0.4.87+curl-8.19.0
[INFO] [stderr]   Downloaded hts-sys v2.2.0
[INFO] [stderr]   Downloaded openssl-src v300.6.0+3.6.2
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+1.95.0" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] [stdout] 9be661aad9105c78578dc5e21412e2ecc89a2c070ff92a9477c4625ce8402505
[INFO] running `Command { std: "docker" "start" "-a" "9be661aad9105c78578dc5e21412e2ecc89a2c070ff92a9477c4625ce8402505", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "9be661aad9105c78578dc5e21412e2ecc89a2c070ff92a9477c4625ce8402505", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "9be661aad9105c78578dc5e21412e2ecc89a2c070ff92a9477c4625ce8402505", kill_on_drop: false }`
[INFO] [stdout] 9be661aad9105c78578dc5e21412e2ecc89a2c070ff92a9477c4625ce8402505
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-tc1/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-4-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:d429b63d4308055ea97f60fb1d3dfca48854a00942f1bd2ad806beaf015945ec" "/opt/rustwide/cargo-home/bin/cargo" "+1.95.0" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 2d76b514f563c7e71b3170d0fd77d6f9ffff634dbaaa85259835dcc95eb68335
[INFO] running `Command { std: "docker" "start" "-a" "2d76b514f563c7e71b3170d0fd77d6f9ffff634dbaaa85259835dcc95eb68335", kill_on_drop: false }`
[INFO] [stderr]    Compiling syn v1.0.109
[INFO] [stderr]     Checking regex-syntax v0.8.10
[INFO] [stderr]     Checking aho-corasick v1.1.4
[INFO] [stderr]    Compiling pkg-config v0.3.33
[INFO] [stderr]     Checking either v1.15.0
[INFO] [stderr]    Compiling libc v0.2.186
[INFO] [stderr]    Compiling target-features v0.1.6
[INFO] [stderr]    Compiling bytemuck_derive v1.10.2
[INFO] [stderr]     Checking getrandom v0.3.4
[INFO] [stderr]    Compiling smartstring v1.0.1
[INFO] [stderr]    Compiling polars-utils v0.36.2
[INFO] [stderr]     Checking simdutf8 v0.1.5
[INFO] [stderr]     Checking chrono v0.4.44
[INFO] [stderr]    Compiling polars-arrow v0.36.2
[INFO] [stderr]    Compiling rustix v1.1.4
[INFO] [stderr]    Compiling serde_core v1.0.228
[INFO] [stderr]     Checking rayon v1.12.0
[INFO] [stderr]     Checking rand_distr v0.4.3
[INFO] [stderr]     Checking ahash v0.8.12
[INFO] [stderr]     Checking streaming-iterator v0.1.9
[INFO] [stderr]     Checking dyn-clone v1.0.20
[INFO] [stderr]     Checking foreign_vec v0.1.0
[INFO] [stderr]     Checking fast-float v0.2.0
[INFO] [stderr]     Checking atoi_simd v0.15.6
[INFO] [stderr]     Checking bitflags v2.11.1
[INFO] [stderr]     Checking strength_reduce v0.2.4
[INFO] [stderr]     Checking ethnum v1.5.3
[INFO] [stderr]    Compiling polars-compute v0.36.2
[INFO] [stderr]    Compiling glob v0.3.3
[INFO] [stderr]    Compiling polars-core v0.36.2
[INFO] [stderr]    Compiling polars-ops v0.36.2
[INFO] [stderr]    Compiling memchr v2.8.0
[INFO] [stderr]     Checking xxhash-rust v0.8.15
[INFO] [stderr]    Compiling libloading v0.8.9
[INFO] [stderr]     Checking argminmax v0.6.3
[INFO] [stderr]    Compiling matrixmultiply v0.3.10
[INFO] [stderr]    Compiling bindgen v0.69.5
[INFO] [stderr]     Checking regex-automata v0.4.14
[INFO] [stderr]    Compiling itertools v0.12.1
[INFO] [stderr]     Checking atoi v2.0.0
[INFO] [stderr]    Compiling clang-sys v1.8.1
[INFO] [stderr]    Compiling jobserver v0.1.34
[INFO] [stderr]     Checking now v0.1.3
[INFO] [stderr]    Compiling nom v7.1.3
[INFO] [stderr]     Checking num-integer v0.1.46
[INFO] [stderr]     Checking num-complex v0.4.6
[INFO] [stderr]    Compiling cc v1.2.61
[INFO] [stderr]     Checking crossterm v0.29.0
[INFO] [stderr]    Compiling lazycell v1.3.0
[INFO] [stderr]    Compiling rustc-hash v1.1.0
[INFO] [stderr]     Checking bytemuck v1.25.0
[INFO] [stderr]    Compiling quick-error v1.2.3
[INFO] [stderr]    Compiling strum_macros v0.25.3
[INFO] [stderr]    Compiling fs-utils v1.1.4
[INFO] [stderr]     Checking comfy-table v7.2.2
[INFO] [stderr]     Checking safe_arch v0.7.4
[INFO] [stderr]    Compiling newtype_derive v0.1.6
[INFO] [stderr]     Checking memmap2 v0.7.1
[INFO] [stderr]    Compiling polars-plan v0.36.2
[INFO] [stderr]     Checking num-rational v0.4.2
[INFO] [stderr]    Compiling strum_macros v0.26.4
[INFO] [stderr]     Checking wide v0.7.33
[INFO] [stderr]    Compiling derive-new v0.6.0
[INFO] [stderr]     Checking hashbrown v0.14.5
[INFO] [stderr]    Compiling polars-lazy v0.36.2
[INFO] [stderr]     Checking simd-adler32 v0.3.9
[INFO] [stderr]     Checking miniz_oxide v0.8.9
[INFO] [stderr]    Compiling enum-map-derive v0.17.0
[INFO] [stderr]    Compiling polars v0.36.2
[INFO] [stderr]     Checking csv-core v0.1.13
[INFO] [stderr]     Checking custom_derive v0.1.7
[INFO] [stderr]    Compiling cmake v0.1.58
[INFO] [stderr]    Compiling openssl-src v300.6.0+3.6.2
[INFO] [stderr]     Checking bit-vec v0.6.3
[INFO] [stderr]     Checking fixedbitset v0.4.2
[INFO] [stderr]     Checking petgraph v0.6.5
[INFO] [stderr]     Checking enum-map v2.7.3
[INFO] [stderr]     Checking time v0.3.47
[INFO] [stderr]     Checking flate2 v1.1.9
[INFO] [stderr]     Checking ndarray v0.15.6
[INFO] [stderr]     Checking bit-set v0.5.3
[INFO] [stderr]     Checking fxhash v0.2.1
[INFO] [stderr]     Checking atomic v0.6.1
[INFO] [stderr]    Compiling clap_derive v4.6.1
[INFO] [stderr]     Checking console v0.15.11
[INFO] [stderr]     Checking itertools v0.11.0
[INFO] [stderr]     Checking serde v1.0.228
[INFO] [stderr]     Checking regex v1.12.3
[INFO] [stderr]    Compiling libz-sys v1.1.28
[INFO] [stderr]    Compiling openssl-sys v0.9.114
[INFO] [stderr]     Checking polars-error v0.36.2
[INFO] [stderr]    Compiling curl-sys v0.4.87+curl-8.19.0
[INFO] [stderr]    Compiling lzma-sys v0.1.20
[INFO] [stderr]    Compiling bzip2-sys v0.1.13+1.0.8
[INFO] [stderr]    Compiling cexpr v0.6.0
[INFO] [stderr]     Checking simba v0.6.0
[INFO] [stderr]     Checking multimap v0.9.1
[INFO] [stderr]     Checking bv v0.11.1
[INFO] [stderr]     Checking bio-types v1.0.4
[INFO] [stderr]     Checking tracing-serde v0.2.0
[INFO] [stderr]     Checking vec_map v0.8.2
[INFO] [stderr]     Checking matchers v0.2.0
[INFO] [stderr]     Checking serde_json v1.0.149
[INFO] [stderr]     Checking csv v1.4.0
[INFO] [stderr]     Checking itertools-num v0.1.3
[INFO] [stderr]     Checking ordered-float v3.9.2
[INFO] [stderr]     Checking crossbeam-channel v0.5.15
[INFO] [stderr]     Checking crossbeam-queue v0.3.12
[INFO] [stderr]     Checking editdistancek v1.0.2
[INFO] [stderr]     Checking ieee754 v0.2.6
[INFO] [stderr]     Checking triple_accel v0.4.0
[INFO] [stderr]     Checking linear-map v1.2.0
[INFO] [stderr]     Checking bytecount v0.6.9
[INFO] [stderr]     Checking strum v0.25.0
[INFO] [stderr]     Checking indicatif v0.17.11
[INFO] [stderr]     Checking crossbeam v0.8.4
[INFO] [stderr]     Checking bam v0.1.4
[INFO] [stderr]     Checking uuid v1.23.1
[INFO] [stderr]     Checking colored v2.2.0
[INFO] [stderr]     Checking num_cpus v1.17.0
[INFO] [stderr]     Checking tracing-subscriber v0.3.23
[INFO] [stderr]     Checking clap v4.6.1
[INFO] [stderr]    Compiling multiversion-macros v0.7.4
[INFO] [stderr]    Compiling nalgebra-macros v0.1.0
[INFO] [stderr]    Compiling derive-new v0.5.9
[INFO] [stderr]     Checking multiversion v0.7.4
[INFO] [stderr]     Checking nalgebra v0.29.0
[INFO] [stderr]    Compiling hts-sys v2.2.0
[INFO] [stderr]     Checking polars-row v0.36.2
[INFO] [stderr]     Checking statrs v0.16.1
[INFO] [stderr]     Checking bio v1.6.0
[INFO] [stderr]     Checking polars-time v0.36.2
[INFO] [stderr]     Checking polars-io v0.36.2
[INFO] [stderr]     Checking rust-htslib v0.47.1
[INFO] [stderr]     Checking bam_stat v0.1.3 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]    --> src/bam_concordance.rs:426:14
[INFO] [stdout]     |
[INFO] [stdout] 426 |         for (i, record) in bam_reader.records().enumerate() {
[INFO] [stdout]     |              ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]    --> src/bam_concordance.rs:459:14
[INFO] [stdout]     |
[INFO] [stdout] 459 |         for (i, record) in bam_reader.records().enumerate() {
[INFO] [stdout]     |              ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]    --> src/common/file_reader/fasta_reader.rs:142:14
[INFO] [stdout]     |
[INFO] [stdout] 142 |         for (i, v) in iter.into_iter().enumerate() {
[INFO] [stdout]     |              ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable pattern
[INFO] [stdout]   --> src/main.rs:14:9
[INFO] [stdout]    |
[INFO] [stdout] 11 |         Subcommands::BamConcordance(bam_concordance_args) => {
[INFO] [stdout]    |         ------------------------------------------------- matches all the relevant values
[INFO] [stdout] ...
[INFO] [stdout] 14 |         _ => panic!("Not Implemented yet"),
[INFO] [stdout]    |         ^ no value can reach this
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unreachable_patterns)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `AlignedRecord` is never constructed
[INFO] [stdout]   --> src/common/bam_ext.rs:97:12
[INFO] [stdout]    |
[INFO] [stdout] 97 | pub struct AlignedRecord<'a> {
[INFO] [stdout]    |            ^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `new`, `compute_effective_coverage`, and `compute_identity` are never used
[INFO] [stdout]    --> src/common/bam_ext.rs:102:12
[INFO] [stdout]     |
[INFO] [stdout] 101 | impl<'a> AlignedRecord<'a>{
[INFO] [stdout]     | -------------------------- associated items in this implementation
[INFO] [stdout] 102 |     pub fn new(record: &'a Record) -> Self {
[INFO] [stdout]     |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 107 |     pub fn compute_effective_coverage(&self) -> f32 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 126 |     pub fn compute_identity(&self) -> f32 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `within_the_range` and `get_regions` are never used
[INFO] [stdout]    --> src/common/file_reader/bed_reader.rs:85:12
[INFO] [stdout]     |
[INFO] [stdout]  63 | impl BedInfo {
[INFO] [stdout]     | ------------ methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout]  85 |     pub fn within_the_range(&self, chromosome: &str, begin_end: &(usize, usize)) -> bool{
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 128 |     pub fn get_regions(&self, chrom: &str) -> Option<&Vec<(usize, usize)>> {
[INFO] [stdout]     |            ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `alt_bases` and `phred_q` are never read
[INFO] [stdout]  --> src/common/file_reader/vcf_reader.rs:8:9
[INFO] [stdout]   |
[INFO] [stdout] 4 | pub struct VcfRowData {
[INFO] [stdout]   |            ---------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 8 |     pub alt_bases: String,
[INFO] [stdout]   |         ^^^^^^^^^
[INFO] [stdout] 9 |     pub phred_q: u32,
[INFO] [stdout]   |         ^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `VcfRowData` 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 `range_hit` is never used
[INFO] [stdout]    --> src/common/file_reader/vcf_reader.rs:113:12
[INFO] [stdout]     |
[INFO] [stdout]  92 | impl VcfInfo {
[INFO] [stdout]     | ------------ method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 113 |     pub fn range_hit(&self, chromosome: &str, range: &(usize, usize)) -> bool {
[INFO] [stdout]     |            ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `get_ref_seq` is never used
[INFO] [stdout]    --> src/common/file_reader/fasta_reader.rs:118:12
[INFO] [stdout]     |
[INFO] [stdout] 109 | impl FastaFile {
[INFO] [stdout]     | -------------- method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 118 |     pub fn get_ref_seq(&self, refname: &str) -> Option<&str> {
[INFO] [stdout]     |            ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `0`, `1`, and `2` are never read
[INFO] [stdout]  --> src/common/file_reader/fastq_reader.rs:7:24
[INFO] [stdout]   |
[INFO] [stdout] 7 | pub struct FastqRecord(pub String, pub String, pub String);
[INFO] [stdout]   |            ----------- ^^^^^^^^^^  ^^^^^^^^^^  ^^^^^^^^^^
[INFO] [stdout]   |            |
[INFO] [stdout]   |            fields in this struct
[INFO] [stdout]   |
[INFO] [stdout]   = help: consider removing these fields
[INFO] [stdout]   = note: `FastqRecord` 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 `eqaul` is never used
[INFO] [stdout]   --> src/common/file_reader/fastq_reader.rs:11:12
[INFO] [stdout]    |
[INFO] [stdout]  9 | impl FastqRecord {
[INFO] [stdout]    | ---------------- method in this implementation
[INFO] [stdout] 10 |
[INFO] [stdout] 11 |     pub fn eqaul(&self, other: &FastqRecord) -> bool {
[INFO] [stdout]    |            ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable pattern
[INFO] [stdout]   --> src/main.rs:14:9
[INFO] [stdout]    |
[INFO] [stdout] 11 |         Subcommands::BamConcordance(bam_concordance_args) => {
[INFO] [stdout]    |         ------------------------------------------------- matches all the relevant values
[INFO] [stdout] ...
[INFO] [stdout] 14 |         _ => panic!("Not Implemented yet"),
[INFO] [stdout]    |         ^ no value can reach this
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unreachable_patterns)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `AlignedRecord` is never constructed
[INFO] [stdout]   --> src/common/bam_ext.rs:97:12
[INFO] [stdout]    |
[INFO] [stdout] 97 | pub struct AlignedRecord<'a> {
[INFO] [stdout]    |            ^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `new`, `compute_effective_coverage`, and `compute_identity` are never used
[INFO] [stdout]    --> src/common/bam_ext.rs:102:12
[INFO] [stdout]     |
[INFO] [stdout] 101 | impl<'a> AlignedRecord<'a>{
[INFO] [stdout]     | -------------------------- associated items in this implementation
[INFO] [stdout] 102 |     pub fn new(record: &'a Record) -> Self {
[INFO] [stdout]     |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 107 |     pub fn compute_effective_coverage(&self) -> f32 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 126 |     pub fn compute_identity(&self) -> f32 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `within_the_range` and `get_regions` are never used
[INFO] [stdout]    --> src/common/file_reader/bed_reader.rs:85:12
[INFO] [stdout]     |
[INFO] [stdout]  63 | impl BedInfo {
[INFO] [stdout]     | ------------ methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout]  85 |     pub fn within_the_range(&self, chromosome: &str, begin_end: &(usize, usize)) -> bool{
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 128 |     pub fn get_regions(&self, chrom: &str) -> Option<&Vec<(usize, usize)>> {
[INFO] [stdout]     |            ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `alt_bases` and `phred_q` are never read
[INFO] [stdout]  --> src/common/file_reader/vcf_reader.rs:8:9
[INFO] [stdout]   |
[INFO] [stdout] 4 | pub struct VcfRowData {
[INFO] [stdout]   |            ---------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 8 |     pub alt_bases: String,
[INFO] [stdout]   |         ^^^^^^^^^
[INFO] [stdout] 9 |     pub phred_q: u32,
[INFO] [stdout]   |         ^^^^^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `VcfRowData` 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 `range_hit` is never used
[INFO] [stdout]    --> src/common/file_reader/vcf_reader.rs:113:12
[INFO] [stdout]     |
[INFO] [stdout]  92 | impl VcfInfo {
[INFO] [stdout]     | ------------ method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 113 |     pub fn range_hit(&self, chromosome: &str, range: &(usize, usize)) -> bool {
[INFO] [stdout]     |            ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `get_ref_seq` is never used
[INFO] [stdout]    --> src/common/file_reader/fasta_reader.rs:118:12
[INFO] [stdout]     |
[INFO] [stdout] 109 | impl FastaFile {
[INFO] [stdout]     | -------------- method in this implementation
[INFO] [stdout] ...
[INFO] [stdout] 118 |     pub fn get_ref_seq(&self, refname: &str) -> Option<&str> {
[INFO] [stdout]     |            ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `FastqRecord` is never constructed
[INFO] [stdout]  --> src/common/file_reader/fastq_reader.rs:7:12
[INFO] [stdout]   |
[INFO] [stdout] 7 | pub struct FastqRecord(pub String, pub String, pub String);
[INFO] [stdout]   |            ^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: method `eqaul` is never used
[INFO] [stdout]   --> src/common/file_reader/fastq_reader.rs:11:12
[INFO] [stdout]    |
[INFO] [stdout]  9 | impl FastqRecord {
[INFO] [stdout]    | ---------------- method in this implementation
[INFO] [stdout] 10 |
[INFO] [stdout] 11 |     pub fn eqaul(&self, other: &FastqRecord) -> bool {
[INFO] [stdout]    |            ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `FastqReaderIter` is never constructed
[INFO] [stdout]   --> src/common/file_reader/fastq_reader.rs:17:12
[INFO] [stdout]    |
[INFO] [stdout] 17 | pub struct FastqReaderIter<'a> {
[INFO] [stdout]    |            ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `new` and `read_one_line` are never used
[INFO] [stdout]   --> src/common/file_reader/fastq_reader.rs:22:12
[INFO] [stdout]    |
[INFO] [stdout] 21 | impl<'a> FastqReaderIter<'a>{
[INFO] [stdout]    | ---------------------------- associated items in this implementation
[INFO] [stdout] 22 |     pub fn new(reader: &'a mut dyn BufRead) -> Self {
[INFO] [stdout]    |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 26 |     fn read_one_line(&mut self) -> Option<String> {
[INFO] [stdout]    |        ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 3m 32s
[INFO] running `Command { std: "docker" "inspect" "2d76b514f563c7e71b3170d0fd77d6f9ffff634dbaaa85259835dcc95eb68335", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "2d76b514f563c7e71b3170d0fd77d6f9ffff634dbaaa85259835dcc95eb68335", kill_on_drop: false }`
[INFO] [stdout] 2d76b514f563c7e71b3170d0fd77d6f9ffff634dbaaa85259835dcc95eb68335
