[INFO] cloning repository https://github.com/stela2502/quantify_bam
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/stela2502/quantify_bam" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fquantify_bam", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fquantify_bam'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 878a12c376d9c628d706e449a74f62655b6e66c7
[INFO] checking stela2502/quantify_bam against master#642c19bfc3a5c1de985bf5d0cc8207ac9d22708a for pr-148577
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fstela2502%2Fquantify_bam" "/workspace/builds/worker-6-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-6-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/stela2502/quantify_bam
[INFO] finished tweaking git repo https://github.com/stela2502/quantify_bam
[INFO] tweaked toml for git repo https://github.com/stela2502/quantify_bam written to /workspace/builds/worker-6-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/stela2502/quantify_bam on toolchain 642c19bfc3a5c1de985bf5d0cc8207ac9d22708a
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+642c19bfc3a5c1de985bf5d0cc8207ac9d22708a" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/stela2502/quantify_bam 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" "+642c19bfc3a5c1de985bf5d0cc8207ac9d22708a" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] [stdout] warning: unexpected `cfg` condition value: `write`
[INFO] [stdout]  --> src/value.rs:4:12
[INFO] [stdout]   |
[INFO] [stdout] 4 | #[cfg_attr(feature = "write", derive(Serialize, Deserialize))]
[INFO] [stdout]   |            ^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]   |
[INFO] [stdout]   = note: no expected values for `feature`
[INFO] [stdout]   = help: consider adding `write` as a feature in `Cargo.toml`
[INFO] [stdout]   = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout]   = note: `#[warn(unexpected_cfgs)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unexpected `cfg` condition value: `write`
[INFO] [stdout]  --> src/value.rs:4:12
[INFO] [stdout]   |
[INFO] [stdout] 4 | #[cfg_attr(feature = "write", derive(Serialize, Deserialize))]
[INFO] [stdout]   |            ^^^^^^^^^^^^^^^^^ help: remove the condition
[INFO] [stdout]   |
[INFO] [stdout]   = note: no expected values for `feature`
[INFO] [stdout]   = help: consider adding `write` as a feature in `Cargo.toml`
[INFO] [stdout]   = note: see <https://doc.rust-lang.org/nightly/rustc/check-cfg/cargo-specifics.html> for more information about checking conditional configuration
[INFO] [stdout]   = note: `#[warn(unexpected_cfgs)]` on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rustody::analysis::bam_flag::BamFlag`
[INFO] [stdout]   --> src/main_logics.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | use rustody::analysis::bam_flag::BamFlag;
[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: `rustody::analysis::bam_flag::BamFlag`
[INFO] [stdout]   --> src/main_logics.rs:17:5
[INFO] [stdout]    |
[INFO] [stdout] 17 | use rustody::analysis::bam_flag::BamFlag;
[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: `Cigar` and `Record`
[INFO] [stdout]   --> src/main_logics.rs:22:46
[INFO] [stdout]    |
[INFO] [stdout] 22 | use rust_htslib::bam::{Reader,Read, record::{Record, Cigar}};
[INFO] [stdout]    |                                              ^^^^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Cigar` and `Record`
[INFO] [stdout]   --> src/main_logics.rs:22:46
[INFO] [stdout]    |
[INFO] [stdout] 22 | use rust_htslib::bam::{Reader,Read, record::{Record, Cigar}};
[INFO] [stdout]    |                                              ^^^^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]    --> src/main_logics.rs:424:17
[INFO] [stdout]     |
[INFO] [stdout] 423 |                   todo!("Handle this case when I have more brainpower.");
[INFO] [stdout]     |                   ------------------------------------------------------ any code following this expression is unreachable
[INFO] [stdout] 424 | /                 let mate_gene_result = match match_type {
[INFO] [stdout] 425 | |                     MatchType::Overlap => gtf.match_cigar_to_gene_overlap(
[INFO] [stdout] 426 | |                         &mate.chromosome,
[INFO] [stdout] 427 | |                         &mate.cigar,
[INFO] [stdout] ...   |
[INFO] [stdout] 436 | |                     ),
[INFO] [stdout] 437 | |                 };
[INFO] [stdout]     | |__________________^ unreachable statement
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unreachable_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unreachable statement
[INFO] [stdout]    --> src/main_logics.rs:424:17
[INFO] [stdout]     |
[INFO] [stdout] 423 |                   todo!("Handle this case when I have more brainpower.");
[INFO] [stdout]     |                   ------------------------------------------------------ any code following this expression is unreachable
[INFO] [stdout] 424 | /                 let mate_gene_result = match match_type {
[INFO] [stdout] 425 | |                     MatchType::Overlap => gtf.match_cigar_to_gene_overlap(
[INFO] [stdout] 426 | |                         &mate.chromosome,
[INFO] [stdout] 427 | |                         &mate.cigar,
[INFO] [stdout] ...   |
[INFO] [stdout] 436 | |                     ),
[INFO] [stdout] 437 | |                 };
[INFO] [stdout]     | |__________________^ unreachable statement
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unreachable_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `fully_matched_exons` is never read
[INFO] [stdout]    --> src/gtf/gene.rs:139:21
[INFO] [stdout]     |
[INFO] [stdout] 139 |                     fully_matched_exons += 1;
[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 `fully_matched_exons` is never read
[INFO] [stdout]    --> src/gtf/gene.rs:177:21
[INFO] [stdout]     |
[INFO] [stdout] 177 |                     fully_matched_exons += 1;
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: maybe it is overwritten before being read?
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `fully_matched_exons` is never read
[INFO] [stdout]    --> src/gtf/gene.rs:139:21
[INFO] [stdout]     |
[INFO] [stdout] 139 |                     fully_matched_exons += 1;
[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 `fully_matched_exons` is never read
[INFO] [stdout]    --> src/gtf/gene.rs:177:21
[INFO] [stdout]     |
[INFO] [stdout] 177 |                     fully_matched_exons += 1;
[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/main_logics.rs:139:9
[INFO] [stdout]     |
[INFO] [stdout] 139 |     let mut reader = Reader::from_path( bam_file  ).unwrap();
[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/main_logics.rs:139:9
[INFO] [stdout]     |
[INFO] [stdout] 139 |     let mut reader = Reader::from_path( bam_file  ).unwrap();
[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: unused variable: `header_view`
[INFO] [stdout]    --> src/main_logics.rs:140:9
[INFO] [stdout]     |
[INFO] [stdout] 140 |     let header_view = Header::from_template(reader.header() );
[INFO] [stdout]     |         ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_header_view`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `header_view`
[INFO] [stdout]    --> src/main_logics.rs:140:9
[INFO] [stdout]     |
[INFO] [stdout] 140 |     let header_view = Header::from_template(reader.header() );
[INFO] [stdout]     |         ^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_header_view`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mate`
[INFO] [stdout]    --> src/main_logics.rs:422:25
[INFO] [stdout]     |
[INFO] [stdout] 422 |             if let Some(mate) = mate_read {
[INFO] [stdout]     |                         ^^^^ help: if this is intentional, prefix it with an underscore: `_mate`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mate`
[INFO] [stdout]    --> src/main_logics.rs:422:25
[INFO] [stdout]     |
[INFO] [stdout] 422 |             if let Some(mate) = mate_read {
[INFO] [stdout]     |                         ^^^^ help: if this is intentional, prefix it with an underscore: `_mate`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mate_gene_result`
[INFO] [stdout]    --> src/main_logics.rs:424:21
[INFO] [stdout]     |
[INFO] [stdout] 424 |                 let mate_gene_result = match match_type {
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_result`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mate_gene_result`
[INFO] [stdout]    --> src/main_logics.rs:424:21
[INFO] [stdout]     |
[INFO] [stdout] 424 |                 let mate_gene_result = match match_type {
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_result`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mate_gene_ids`
[INFO] [stdout]    --> src/main_logics.rs:439:21
[INFO] [stdout]     |
[INFO] [stdout] 439 |                 let mate_gene_ids = extract_gene_ids(&mate_gene_result, mate, mapping_info);
[INFO] [stdout]     |                     ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_ids`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mate_gene_ids`
[INFO] [stdout]    --> src/main_logics.rs:439:21
[INFO] [stdout]     |
[INFO] [stdout] 439 |                 let mate_gene_ids = extract_gene_ids(&mate_gene_result, mate, mapping_info);
[INFO] [stdout]     |                     ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_ids`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mate_gene_id`
[INFO] [stdout]    --> src/main_logics.rs:441:21
[INFO] [stdout]     |
[INFO] [stdout] 441 |                 for mate_gene_id in &mate_gene_ids {
[INFO] [stdout]     |                     ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_id`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mate_gene_id`
[INFO] [stdout]    --> src/main_logics.rs:441:21
[INFO] [stdout]     |
[INFO] [stdout] 441 |                 for mate_gene_id in &mate_gene_ids {
[INFO] [stdout]     |                     ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_id`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mate_gene_id_u64`
[INFO] [stdout]    --> src/main_logics.rs:442:25
[INFO] [stdout]     |
[INFO] [stdout] 442 |                     let mate_gene_id_u64 = exp_idx.get_gene_id(mate_gene_id);
[INFO] [stdout]     |                         ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_id_u64`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mate_guh`
[INFO] [stdout]    --> src/main_logics.rs:443:25
[INFO] [stdout]     |
[INFO] [stdout] 443 |                     let mate_guh = GeneUmiHash(mate_gene_id_u64, mate.umi);
[INFO] [stdout]     |                         ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_guh`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `processor`
[INFO] [stdout]    --> src/main_logics.rs:446:37
[INFO] [stdout]     |
[INFO] [stdout] 446 |                         if let Some(processor) = mutations {
[INFO] [stdout]     |                                     ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_processor`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mate_gene_id_u64`
[INFO] [stdout]    --> src/main_logics.rs:442:25
[INFO] [stdout]     |
[INFO] [stdout] 442 |                     let mate_gene_id_u64 = exp_idx.get_gene_id(mate_gene_id);
[INFO] [stdout]     |                         ^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_gene_id_u64`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `mate_guh`
[INFO] [stdout]    --> src/main_logics.rs:443:25
[INFO] [stdout]     |
[INFO] [stdout] 443 |                     let mate_guh = GeneUmiHash(mate_gene_id_u64, mate.umi);
[INFO] [stdout]     |                         ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_mate_guh`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `processor`
[INFO] [stdout]    --> src/main_logics.rs:446:37
[INFO] [stdout]     |
[INFO] [stdout] 446 |                         if let Some(processor) = mutations {
[INFO] [stdout]     |                                     ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_processor`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [unoptimized + debuginfo] target(s) in 1m 30s
[INFO] running `Command { std: "docker" "inspect" "ea4607d12686729d49c0589eac3a09a8998e759ec1fa8dba57c75f92c364fb41", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ea4607d12686729d49c0589eac3a09a8998e759ec1fa8dba57c75f92c364fb41", kill_on_drop: false }`
[INFO] [stdout] ea4607d12686729d49c0589eac3a09a8998e759ec1fa8dba57c75f92c364fb41
