[INFO] cloning repository https://github.com/bluenote-1577/rs-liftover
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/bluenote-1577/rs-liftover" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Frs-liftover", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Frs-liftover'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] f54a6a838f3d2656e270465c5d5d14a3885d640c
[INFO] testing bluenote-1577/rs-liftover against try#c2e32f1c9652b13ed99608599c1e855462f421f3 for pr-146098-7
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Frs-liftover" "/workspace/builds/worker-1-tc2/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-1-tc2/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/bluenote-1577/rs-liftover
[INFO] finished tweaking git repo https://github.com/bluenote-1577/rs-liftover
[INFO] tweaked toml for git repo https://github.com/bluenote-1577/rs-liftover written to /workspace/builds/worker-1-tc2/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/bluenote-1577/rs-liftover on toolchain c2e32f1c9652b13ed99608599c1e855462f421f3
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+c2e32f1c9652b13ed99608599c1e855462f421f3" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/bluenote-1577/rs-liftover 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" "+c2e32f1c9652b13ed99608599c1e855462f421f3" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "start" "-a" "8353ad692b78ce03bfb0e65a71a83aa2034862920a08f09ec96430343567bd3f", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "8353ad692b78ce03bfb0e65a71a83aa2034862920a08f09ec96430343567bd3f", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "8353ad692b78ce03bfb0e65a71a83aa2034862920a08f09ec96430343567bd3f", kill_on_drop: false }`
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[INFO] [stderr]    Compiling rs-liftover v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `Header`
[INFO] [stdout]  --> src/parse_files.rs:6:32
[INFO] [stdout]   |
[INFO] [stdout] 6 | use rust_htslib::bam::header::{Header, HeaderRecord};
[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 imports: `Deserialize` and `Serialize`
[INFO] [stdout]  --> src/parse_files.rs:9:13
[INFO] [stdout]   |
[INFO] [stdout] 9 | use serde::{Deserialize, Serialize};
[INFO] [stdout]   |             ^^^^^^^^^^^  ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs`
[INFO] [stdout]   --> src/parse_files.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use std::fs;
[INFO] [stdout]    |     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::prelude::*`
[INFO] [stdout]   --> src/parse_files.rs:14:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | use std::io::prelude::*;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::sync::Mutex`
[INFO] [stdout]   --> src/parse_files.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | use std::sync::Mutex;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `App` and `SubCommand`
[INFO] [stdout]  --> src/main.rs:3:12
[INFO] [stdout]   |
[INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stdout]   |            ^^^                             ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `clap::App`: Replaced with `Command`
[INFO] [stdout]  --> src/main.rs:3:12
[INFO] [stdout]   |
[INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stdout]   |            ^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `clap::SubCommand`: Replaced with `Command::new` unless you intended the `Subcommand` trait
[INFO] [stdout]  --> src/main.rs:3:44
[INFO] [stdout]   |
[INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stdout]   |                                            ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated unit variant `clap::AppSettings::ArgRequiredElseHelp`: Replaced with `Command::arg_required_else_help` and `Command::is_arg_required_else_help_set`
[INFO] [stdout]  --> src/main.rs:7:31
[INFO] [stdout]   |
[INFO] [stdout] 7 |         .setting(AppSettings::ArgRequiredElseHelp)
[INFO] [stdout]   |                               ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/parse_files.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/parse_files.rs:229:17
[INFO] [stdout]     |
[INFO] [stdout] 229 |             let mut gap_len = 0;
[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/parse_files.rs:232:17
[INFO] [stdout]     |
[INFO] [stdout] 232 |             let mut new_start_pos = 0;
[INFO] [stdout]     |                 ----^^^^^^^^^^^^^
[INFO] [stdout]     |                 |
[INFO] [stdout]     |                 help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `aligned_pairs`
[INFO] [stdout]    --> src/parse_files.rs:214:17
[INFO] [stdout]     |
[INFO] [stdout] 214 |             let aligned_pairs = record.aligned_pairs();
[INFO] [stdout]     |                 ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_aligned_pairs`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `curr_read_pos`
[INFO] [stdout]    --> src/parse_files.rs:224:17
[INFO] [stdout]     |
[INFO] [stdout] 224 |             let curr_read_pos = cigar.leading_softclips();
[INFO] [stdout]     |                 ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_curr_read_pos`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `gap_len`
[INFO] [stdout]    --> src/parse_files.rs:229:17
[INFO] [stdout]     |
[INFO] [stdout] 229 |             let mut gap_len = 0;
[INFO] [stdout]     |                 ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_gap_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `new_start_pos`
[INFO] [stdout]    --> src/parse_files.rs:232:17
[INFO] [stdout]     |
[INFO] [stdout] 232 |             let mut new_start_pos = 0;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_new_start_pos`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:263:49
[INFO] [stdout]     |
[INFO] [stdout] 263 |                 if matches!(c, hts_Cigar::Match(u32))
[INFO] [stdout]     |                                                 ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:264:51
[INFO] [stdout]     |
[INFO] [stdout] 264 |                     || matches!(c, hts_Cigar::Ins(u32))
[INFO] [stdout]     |                                                   ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:265:51
[INFO] [stdout]     |
[INFO] [stdout] 265 |                     || matches!(c, hts_Cigar::Del(u32))
[INFO] [stdout]     |                                                   ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:270:59
[INFO] [stdout]     |
[INFO] [stdout] 270 | ...                   if matches!(c, hts_Cigar::Ins(u32))
[INFO] [stdout]     |                                                     ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:271:65
[INFO] [stdout]     |
[INFO] [stdout] 271 | ...                   || matches!(c, hts_Cigar::Match(u32))
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:277:55
[INFO] [stdout]     |
[INFO] [stdout] 277 |                         if matches!(c, hts_Cigar::Ins(u32)) {
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:283:65
[INFO] [stdout]     |
[INFO] [stdout] 283 | ...                   if matches!(c, hts_Cigar::Match(u32)) {
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:301:65
[INFO] [stdout]     |
[INFO] [stdout] 301 | ...                   if matches!(c, hts_Cigar::Match(u32)) {
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:315:69
[INFO] [stdout]     |
[INFO] [stdout] 315 | ...                   && matches!(c, hts_Cigar::Match(u32))
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:320:65
[INFO] [stdout]     |
[INFO] [stdout] 320 | ...                   if matches!(c, hts_Cigar::Match(u32)) {
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:323:63
[INFO] [stdout]     |
[INFO] [stdout] 323 | ...                   if matches!(c, hts_Cigar::Del(u32)) {
[INFO] [stdout]     |                                                     ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:344:65
[INFO] [stdout]     |
[INFO] [stdout] 344 | ...                   if matches!(c, hts_Cigar::Match(u32)) {
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:347:63
[INFO] [stdout]     |
[INFO] [stdout] 347 | ...                   if matches!(c, hts_Cigar::Del(u32)) {
[INFO] [stdout]     |                                                     ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `s1`
[INFO] [stdout]    --> src/parse_files.rs:358:17
[INFO] [stdout]     |
[INFO] [stdout] 358 |             let s1 = &secondary_seqs_dict[&cinfo.secondary_name]
[INFO] [stdout]     |                 ^^ help: if this is intentional, prefix it with an underscore: `_s1`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `s2`
[INFO] [stdout]    --> src/parse_files.rs:360:17
[INFO] [stdout]     |
[INFO] [stdout] 360 |             let s2 = &primary_seqs_dict[&cinfo.primary_name]
[INFO] [stdout]     |                 ^^ help: if this is intentional, prefix it with an underscore: `_s2`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `seq_len_from_cig` is assigned to, but never used
[INFO] [stdout]    --> src/parse_files.rs:365:17
[INFO] [stdout]     |
[INFO] [stdout] 365 |             let mut seq_len_from_cig = 0;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_seq_len_from_cig` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:368:53
[INFO] [stdout]     |
[INFO] [stdout] 368 |                 if matches!(cigar, hts_Cigar::Match(u32)) {
[INFO] [stdout]     |                                                     ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:371:58
[INFO] [stdout]     |
[INFO] [stdout] 371 |                 } else if matches!(cigar, hts_Cigar::Ins(u32)) {
[INFO] [stdout]     |                                                          ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:373:63
[INFO] [stdout]     |
[INFO] [stdout] 373 |                 } else if matches!(cigar, hts_Cigar::SoftClip(u32)) {
[INFO] [stdout]     |                                                               ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `seq_len_from_cig` is never read
[INFO] [stdout]    --> src/parse_files.rs:374:21
[INFO] [stdout]     |
[INFO] [stdout] 374 |                     seq_len_from_cig += cigar.len();
[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: value assigned to `seq_len_from_cig` is never read
[INFO] [stdout]    --> src/parse_files.rs:372:21
[INFO] [stdout]     |
[INFO] [stdout] 372 |                     seq_len_from_cig += cigar.len();
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `seq_len_from_cig` is never read
[INFO] [stdout]    --> src/parse_files.rs:369:21
[INFO] [stdout]     |
[INFO] [stdout] 369 |                     seq_len_from_cig += cigar.len();
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [optimized + debuginfo] target(s) in 7m 41s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1`
[INFO] running `Command { std: "docker" "inspect" "b22d41af0190712156992425034f4cef4e1a709c618d3a3f3545a39e98be39f4", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "b22d41af0190712156992425034f4cef4e1a709c618d3a3f3545a39e98be39f4", kill_on_drop: false }`
[INFO] [stdout] b22d41af0190712156992425034f4cef4e1a709c618d3a3f3545a39e98be39f4
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+c2e32f1c9652b13ed99608599c1e855462f421f3" "test" "--frozen" "--no-run" "--message-format=json", kill_on_drop: false }`
[INFO] [stdout] 510022e063e4826c7aa151ecd6a5f00f7598054c45db2f564fe35859cab1e36f
[INFO] running `Command { std: "docker" "start" "-a" "510022e063e4826c7aa151ecd6a5f00f7598054c45db2f564fe35859cab1e36f", kill_on_drop: false }`
[INFO] [stderr]    Compiling rs-liftover v0.1.0 (/opt/rustwide/workdir)
[INFO] [stdout] warning: unused import: `Header`
[INFO] [stdout]  --> src/parse_files.rs:6:32
[INFO] [stdout]   |
[INFO] [stdout] 6 | use rust_htslib::bam::header::{Header, HeaderRecord};
[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 imports: `Deserialize` and `Serialize`
[INFO] [stdout]  --> src/parse_files.rs:9:13
[INFO] [stdout]   |
[INFO] [stdout] 9 | use serde::{Deserialize, Serialize};
[INFO] [stdout]   |             ^^^^^^^^^^^  ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::fs`
[INFO] [stdout]   --> src/parse_files.rs:11:5
[INFO] [stdout]    |
[INFO] [stdout] 11 | use std::fs;
[INFO] [stdout]    |     ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::io::prelude::*`
[INFO] [stdout]   --> src/parse_files.rs:14:5
[INFO] [stdout]    |
[INFO] [stdout] 14 | use std::io::prelude::*;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::sync::Mutex`
[INFO] [stdout]   --> src/parse_files.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | use std::sync::Mutex;
[INFO] [stdout]    |     ^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `App` and `SubCommand`
[INFO] [stdout]  --> src/main.rs:3:12
[INFO] [stdout]   |
[INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stdout]   |            ^^^                             ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `clap::App`: Replaced with `Command`
[INFO] [stdout]  --> src/main.rs:3:12
[INFO] [stdout]   |
[INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stdout]   |            ^^^
[INFO] [stdout]   |
[INFO] [stdout]   = note: `#[warn(deprecated)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated struct `clap::SubCommand`: Replaced with `Command::new` unless you intended the `Subcommand` trait
[INFO] [stdout]  --> src/main.rs:3:44
[INFO] [stdout]   |
[INFO] [stdout] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stdout]   |                                            ^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: use of deprecated unit variant `clap::AppSettings::ArgRequiredElseHelp`: Replaced with `Command::arg_required_else_help` and `Command::is_arg_required_else_help_set`
[INFO] [stdout]  --> src/main.rs:7:31
[INFO] [stdout]   |
[INFO] [stdout] 7 |         .setting(AppSettings::ArgRequiredElseHelp)
[INFO] [stdout]   |                               ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/parse_files.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable does not need to be mutable
[INFO] [stdout]    --> src/parse_files.rs:229:17
[INFO] [stdout]     |
[INFO] [stdout] 229 |             let mut gap_len = 0;
[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/parse_files.rs:232:17
[INFO] [stdout]     |
[INFO] [stdout] 232 |             let mut new_start_pos = 0;
[INFO] [stdout]     |                 ----^^^^^^^^^^^^^
[INFO] [stdout]     |                 |
[INFO] [stdout]     |                 help: remove this `mut`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `aligned_pairs`
[INFO] [stdout]    --> src/parse_files.rs:214:17
[INFO] [stdout]     |
[INFO] [stdout] 214 |             let aligned_pairs = record.aligned_pairs();
[INFO] [stdout]     |                 ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_aligned_pairs`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `curr_read_pos`
[INFO] [stdout]    --> src/parse_files.rs:224:17
[INFO] [stdout]     |
[INFO] [stdout] 224 |             let curr_read_pos = cigar.leading_softclips();
[INFO] [stdout]     |                 ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_curr_read_pos`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `gap_len`
[INFO] [stdout]    --> src/parse_files.rs:229:17
[INFO] [stdout]     |
[INFO] [stdout] 229 |             let mut gap_len = 0;
[INFO] [stdout]     |                 ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_gap_len`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `new_start_pos`
[INFO] [stdout]    --> src/parse_files.rs:232:17
[INFO] [stdout]     |
[INFO] [stdout] 232 |             let mut new_start_pos = 0;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_new_start_pos`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:263:49
[INFO] [stdout]     |
[INFO] [stdout] 263 |                 if matches!(c, hts_Cigar::Match(u32))
[INFO] [stdout]     |                                                 ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:264:51
[INFO] [stdout]     |
[INFO] [stdout] 264 |                     || matches!(c, hts_Cigar::Ins(u32))
[INFO] [stdout]     |                                                   ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:265:51
[INFO] [stdout]     |
[INFO] [stdout] 265 |                     || matches!(c, hts_Cigar::Del(u32))
[INFO] [stdout]     |                                                   ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:270:59
[INFO] [stdout]     |
[INFO] [stdout] 270 | ...                   if matches!(c, hts_Cigar::Ins(u32))
[INFO] [stdout]     |                                                     ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:271:65
[INFO] [stdout]     |
[INFO] [stdout] 271 | ...                   || matches!(c, hts_Cigar::Match(u32))
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:277:55
[INFO] [stdout]     |
[INFO] [stdout] 277 |                         if matches!(c, hts_Cigar::Ins(u32)) {
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:283:65
[INFO] [stdout]     |
[INFO] [stdout] 283 | ...                   if matches!(c, hts_Cigar::Match(u32)) {
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:301:65
[INFO] [stdout]     |
[INFO] [stdout] 301 | ...                   if matches!(c, hts_Cigar::Match(u32)) {
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:315:69
[INFO] [stdout]     |
[INFO] [stdout] 315 | ...                   && matches!(c, hts_Cigar::Match(u32))
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:320:65
[INFO] [stdout]     |
[INFO] [stdout] 320 | ...                   if matches!(c, hts_Cigar::Match(u32)) {
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:323:63
[INFO] [stdout]     |
[INFO] [stdout] 323 | ...                   if matches!(c, hts_Cigar::Del(u32)) {
[INFO] [stdout]     |                                                     ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:344:65
[INFO] [stdout]     |
[INFO] [stdout] 344 | ...                   if matches!(c, hts_Cigar::Match(u32)) {
[INFO] [stdout]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:347:63
[INFO] [stdout]     |
[INFO] [stdout] 347 | ...                   if matches!(c, hts_Cigar::Del(u32)) {
[INFO] [stdout]     |                                                     ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `s1`
[INFO] [stdout]    --> src/parse_files.rs:358:17
[INFO] [stdout]     |
[INFO] [stdout] 358 |             let s1 = &secondary_seqs_dict[&cinfo.secondary_name]
[INFO] [stdout]     |                 ^^ help: if this is intentional, prefix it with an underscore: `_s1`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `s2`
[INFO] [stdout]    --> src/parse_files.rs:360:17
[INFO] [stdout]     |
[INFO] [stdout] 360 |             let s2 = &primary_seqs_dict[&cinfo.primary_name]
[INFO] [stdout]     |                 ^^ help: if this is intentional, prefix it with an underscore: `_s2`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: variable `seq_len_from_cig` is assigned to, but never used
[INFO] [stdout]    --> src/parse_files.rs:365:17
[INFO] [stdout]     |
[INFO] [stdout] 365 |             let mut seq_len_from_cig = 0;
[INFO] [stdout]     |                 ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: consider using `_seq_len_from_cig` instead
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:368:53
[INFO] [stdout]     |
[INFO] [stdout] 368 |                 if matches!(cigar, hts_Cigar::Match(u32)) {
[INFO] [stdout]     |                                                     ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:371:58
[INFO] [stdout]     |
[INFO] [stdout] 371 |                 } else if matches!(cigar, hts_Cigar::Ins(u32)) {
[INFO] [stdout]     |                                                          ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `u32`
[INFO] [stdout]    --> src/parse_files.rs:373:63
[INFO] [stdout]     |
[INFO] [stdout] 373 |                 } else if matches!(cigar, hts_Cigar::SoftClip(u32)) {
[INFO] [stdout]     |                                                               ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `seq_len_from_cig` is never read
[INFO] [stdout]    --> src/parse_files.rs:374:21
[INFO] [stdout]     |
[INFO] [stdout] 374 |                     seq_len_from_cig += cigar.len();
[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: value assigned to `seq_len_from_cig` is never read
[INFO] [stdout]    --> src/parse_files.rs:372:21
[INFO] [stdout]     |
[INFO] [stdout] 372 |                     seq_len_from_cig += cigar.len();
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `seq_len_from_cig` is never read
[INFO] [stdout]    --> src/parse_files.rs:369:21
[INFO] [stdout]     |
[INFO] [stdout] 369 |                     seq_len_from_cig += cigar.len();
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `test` profile [optimized + debuginfo] target(s) in 1.00s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1`
[INFO] running `Command { std: "docker" "inspect" "510022e063e4826c7aa151ecd6a5f00f7598054c45db2f564fe35859cab1e36f", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "510022e063e4826c7aa151ecd6a5f00f7598054c45db2f564fe35859cab1e36f", kill_on_drop: false }`
[INFO] [stdout] 510022e063e4826c7aa151ecd6a5f00f7598054c45db2f564fe35859cab1e36f
[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/target:/opt/rustwide/target:rw,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-1-tc2/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/cargo-home:/opt/rustwide/cargo-home:ro,Z" "-v" "/var/lib/crater-agent-workspace/rustup-home:/opt/rustwide/rustup-home:ro,Z" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-e" "CARGO_INCREMENTAL=0" "-e" "RUST_BACKTRACE=full" "-e" "RUSTFLAGS=--cap-lints=forbid" "-e" "RUSTDOCFLAGS=--cap-lints=forbid" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-w" "/opt/rustwide/workdir" "-m" "1610612736" "--user" "0:0" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:4848fb76d95f26979359cc7e45710b1dbc8f3acb7aeedee7c460d7702230f228" "/opt/rustwide/cargo-home/bin/cargo" "+c2e32f1c9652b13ed99608599c1e855462f421f3" "test" "--frozen", kill_on_drop: false }`
[INFO] [stdout] cacd8ceed1596b2db90c1a6f0976c73b80faf4ced9c35e52c343127df501c3f2
[INFO] running `Command { std: "docker" "start" "-a" "cacd8ceed1596b2db90c1a6f0976c73b80faf4ced9c35e52c343127df501c3f2", kill_on_drop: false }`
[INFO] [stderr] warning: unused import: `Header`
[INFO] [stderr]  --> src/parse_files.rs:6:32
[INFO] [stderr]   |
[INFO] [stderr] 6 | use rust_htslib::bam::header::{Header, HeaderRecord};
[INFO] [stderr]   |                                ^^^^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(unused_imports)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused imports: `Deserialize` and `Serialize`
[INFO] [stderr]  --> src/parse_files.rs:9:13
[INFO] [stderr]   |
[INFO] [stderr] 9 | use serde::{Deserialize, Serialize};
[INFO] [stderr]   |             ^^^^^^^^^^^  ^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::fs`
[INFO] [stderr]   --> src/parse_files.rs:11:5
[INFO] [stderr]    |
[INFO] [stderr] 11 | use std::fs;
[INFO] [stderr]    |     ^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::io::prelude::*`
[INFO] [stderr]   --> src/parse_files.rs:14:5
[INFO] [stderr]    |
[INFO] [stderr] 14 | use std::io::prelude::*;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `std::sync::Mutex`
[INFO] [stderr]   --> src/parse_files.rs:17:5
[INFO] [stderr]    |
[INFO] [stderr] 17 | use std::sync::Mutex;
[INFO] [stderr]    |     ^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused imports: `App` and `SubCommand`
[INFO] [stderr]  --> src/main.rs:3:12
[INFO] [stderr]   |
[INFO] [stderr] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stderr]   |            ^^^                             ^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated struct `clap::App`: Replaced with `Command`
[INFO] [stderr]  --> src/main.rs:3:12
[INFO] [stderr]   |
[INFO] [stderr] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stderr]   |            ^^^
[INFO] [stderr]   |
[INFO] [stderr]   = note: `#[warn(deprecated)]` on by default
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated struct `clap::SubCommand`: Replaced with `Command::new` unless you intended the `Subcommand` trait
[INFO] [stderr]  --> src/main.rs:3:44
[INFO] [stderr]   |
[INFO] [stderr] 3 | use clap::{App, AppSettings, Arg, Command, SubCommand};
[INFO] [stderr]   |                                            ^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: use of deprecated unit variant `clap::AppSettings::ArgRequiredElseHelp`: Replaced with `Command::arg_required_else_help` and `Command::is_arg_required_else_help_set`
[INFO] [stderr]  --> src/main.rs:7:31
[INFO] [stderr]   |
[INFO] [stderr] 7 |         .setting(AppSettings::ArgRequiredElseHelp)
[INFO] [stderr]   |                               ^^^^^^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: unused import: `rayon::prelude`
[INFO] [stderr]  --> src/parse_files.rs:3:5
[INFO] [stderr]   |
[INFO] [stderr] 3 | use rayon::prelude::*;
[INFO] [stderr]   |     ^^^^^^^^^^^^^^
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/parse_files.rs:229:17
[INFO] [stderr]     |
[INFO] [stderr] 229 |             let mut gap_len = 0;
[INFO] [stderr]     |                 ----^^^^^^^
[INFO] [stderr]     |                 |
[INFO] [stderr]     |                 help: remove this `mut`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_mut)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: variable does not need to be mutable
[INFO] [stderr]    --> src/parse_files.rs:232:17
[INFO] [stderr]     |
[INFO] [stderr] 232 |             let mut new_start_pos = 0;
[INFO] [stderr]     |                 ----^^^^^^^^^^^^^
[INFO] [stderr]     |                 |
[INFO] [stderr]     |                 help: remove this `mut`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `aligned_pairs`
[INFO] [stderr]    --> src/parse_files.rs:214:17
[INFO] [stderr]     |
[INFO] [stderr] 214 |             let aligned_pairs = record.aligned_pairs();
[INFO] [stderr]     |                 ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_aligned_pairs`
[INFO] [stderr]     |
[INFO] [stderr]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `curr_read_pos`
[INFO] [stderr]    --> src/parse_files.rs:224:17
[INFO] [stderr]     |
[INFO] [stderr] 224 |             let curr_read_pos = cigar.leading_softclips();
[INFO] [stderr]     |                 ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_curr_read_pos`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `gap_len`
[INFO] [stderr]    --> src/parse_files.rs:229:17
[INFO] [stderr]     |
[INFO] [stderr] 229 |             let mut gap_len = 0;
[INFO] [stderr]     |                 ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_gap_len`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `new_start_pos`
[INFO] [stderr]    --> src/parse_files.rs:232:17
[INFO] [stderr]     |
[INFO] [stderr] 232 |             let mut new_start_pos = 0;
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_new_start_pos`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:263:49
[INFO] [stderr]     |
[INFO] [stderr] 263 |                 if matches!(c, hts_Cigar::Match(u32))
[INFO] [stderr]     |                                                 ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:264:51
[INFO] [stderr]     |
[INFO] [stderr] 264 |                     || matches!(c, hts_Cigar::Ins(u32))
[INFO] [stderr]     |                                                   ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:265:51
[INFO] [stderr]     |
[INFO] [stderr] 265 |                     || matches!(c, hts_Cigar::Del(u32))
[INFO] [stderr]     |                                                   ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:270:59
[INFO] [stderr]     |
[INFO] [stderr] 270 | ...                   if matches!(c, hts_Cigar::Ins(u32))
[INFO] [stderr]     |                                                     ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:271:65
[INFO] [stderr]     |
[INFO] [stderr] 271 | ...                   || matches!(c, hts_Cigar::Match(u32))
[INFO] [stderr]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:277:55
[INFO] [stderr]     |
[INFO] [stderr] 277 |                         if matches!(c, hts_Cigar::Ins(u32)) {
[INFO] [stderr]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:283:65
[INFO] [stderr]     |
[INFO] [stderr] 283 | ...                   if matches!(c, hts_Cigar::Match(u32)) {
[INFO] [stderr]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:301:65
[INFO] [stderr]     |
[INFO] [stderr] 301 | ...                   if matches!(c, hts_Cigar::Match(u32)) {
[INFO] [stderr]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:315:69
[INFO] [stderr]     |
[INFO] [stderr] 315 | ...                   && matches!(c, hts_Cigar::Match(u32))
[INFO] [stderr]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:320:65
[INFO] [stderr]     |
[INFO] [stderr] 320 | ...                   if matches!(c, hts_Cigar::Match(u32)) {
[INFO] [stderr]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:323:63
[INFO] [stderr]     |
[INFO] [stderr] 323 | ...                   if matches!(c, hts_Cigar::Del(u32)) {
[INFO] [stderr]     |                                                     ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:344:65
[INFO] [stderr]     |
[INFO] [stderr] 344 | ...                   if matches!(c, hts_Cigar::Match(u32)) {
[INFO] [stderr]     |                                                       ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:347:63
[INFO] [stderr]     |
[INFO] [stderr] 347 | ...                   if matches!(c, hts_Cigar::Del(u32)) {
[INFO] [stderr]     |                                                     ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `s1`
[INFO] [stderr]    --> src/parse_files.rs:358:17
[INFO] [stderr]     |
[INFO] [stderr] 358 |             let s1 = &secondary_seqs_dict[&cinfo.secondary_name]
[INFO] [stderr]     |                 ^^ help: if this is intentional, prefix it with an underscore: `_s1`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `s2`
[INFO] [stderr]    --> src/parse_files.rs:360:17
[INFO] [stderr]     |
[INFO] [stderr] 360 |             let s2 = &primary_seqs_dict[&cinfo.primary_name]
[INFO] [stderr]     |                 ^^ help: if this is intentional, prefix it with an underscore: `_s2`
[INFO] [stderr] 
[INFO] [stderr] warning: variable `seq_len_from_cig` is assigned to, but never used
[INFO] [stderr]    --> src/parse_files.rs:365:17
[INFO] [stderr]     |
[INFO] [stderr] 365 |             let mut seq_len_from_cig = 0;
[INFO] [stderr]     |                 ^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = note: consider using `_seq_len_from_cig` instead
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:368:53
[INFO] [stderr]     |
[INFO] [stderr] 368 |                 if matches!(cigar, hts_Cigar::Match(u32)) {
[INFO] [stderr]     |                                                     ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:371:58
[INFO] [stderr]     |
[INFO] [stderr] 371 |                 } else if matches!(cigar, hts_Cigar::Ins(u32)) {
[INFO] [stderr]     |                                                          ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: unused variable: `u32`
[INFO] [stderr]    --> src/parse_files.rs:373:63
[INFO] [stderr]     |
[INFO] [stderr] 373 |                 } else if matches!(cigar, hts_Cigar::SoftClip(u32)) {
[INFO] [stderr]     |                                                               ^^^ help: if this is intentional, prefix it with an underscore: `_u32`
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `seq_len_from_cig` is never read
[INFO] [stderr]    --> src/parse_files.rs:374:21
[INFO] [stderr]     |
[INFO] [stderr] 374 |                     seq_len_from_cig += cigar.len();
[INFO] [stderr]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr]     = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `seq_len_from_cig` is never read
[INFO] [stderr]    --> src/parse_files.rs:372:21
[INFO] [stderr]     |
[INFO] [stderr] 372 |                     seq_len_from_cig += cigar.len();
[INFO] [stderr]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: value assigned to `seq_len_from_cig` is never read
[INFO] [stderr]    --> src/parse_files.rs:369:21
[INFO] [stderr]     |
[INFO] [stderr] 369 |                     seq_len_from_cig += cigar.len();
[INFO] [stderr]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stderr]     |
[INFO] [stderr]     = help: maybe it is overwritten before being read?
[INFO] [stderr] 
[INFO] [stderr] warning: `rs-liftover` (bin "rs-liftover" test) generated 38 warnings (run `cargo fix --bin "rs-liftover" -p rs-liftover --tests` to apply 30 suggestions)
[INFO] [stderr]     Finished `test` profile [optimized + debuginfo] target(s) in 0.26s
[INFO] [stderr] warning: the following packages contain code that will be rejected by a future version of Rust: nalgebra v0.27.1
[INFO] [stderr] note: to see what the problems were, use the option `--future-incompat-report`, or run `cargo report future-incompatibilities --id 1`
[INFO] [stderr]      Running unittests src/main.rs (/opt/rustwide/target/debug/deps/rs_liftover-1eaf3bac6fa16d5d)
[INFO] [stdout] 
[INFO] [stdout] running 0 tests
[INFO] [stdout] 
[INFO] [stdout] test result: ok. 0 passed; 0 failed; 0 ignored; 0 measured; 0 filtered out; finished in 0.00s
[INFO] [stdout] 
[INFO] running `Command { std: "docker" "inspect" "cacd8ceed1596b2db90c1a6f0976c73b80faf4ced9c35e52c343127df501c3f2", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "cacd8ceed1596b2db90c1a6f0976c73b80faf4ced9c35e52c343127df501c3f2", kill_on_drop: false }`
[INFO] [stdout] cacd8ceed1596b2db90c1a6f0976c73b80faf4ced9c35e52c343127df501c3f2
