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[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2Fbluenote-1577%2Frs-liftover" "/workspace/builds/worker-2-tc1/source", kill_on_drop: false }`
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[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: Use of ambiguously glob imported trait `Read`
[INFO] [stdout]    --> src/parse_files.rs:184:53
[INFO] [stdout]     |
[INFO] [stdout]   8 | use rust_htslib::bam::*;
[INFO] [stdout]     |     ---------------- `Read` imported ambiguously here
[INFO] [stdout] ...
[INFO] [stdout] 184 |     let mut header = bam::Header::from_template(bam.header());
[INFO] [stdout]     |                                                     ^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: Import `Read` explicitly
[INFO] [stdout]     = warning: this was previously accepted by the compiler but is being phased out; it will become a hard error in a future release!
[INFO] [stdout]     = note: for more information, see issue #147992 <https://github.com/rust-lang/rust/issues/147992>
[INFO] [stdout]     = note: `#[warn(ambiguous_glob_imported_traits)]` (part of `#[warn(future_incompatible)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: Use of ambiguously glob imported trait `Read`
[INFO] [stdout]    --> src/parse_files.rs:198:20
[INFO] [stdout]     |
[INFO] [stdout]   8 | use rust_htslib::bam::*;
[INFO] [stdout]     |     ---------------- `Read` imported ambiguously here
[INFO] [stdout] ...
[INFO] [stdout] 198 |     for rec in bam.records() {
[INFO] [stdout]     |                    ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: Import `Read` explicitly
[INFO] [stdout]     = warning: this was previously accepted by the compiler but is being phased out; it will become a hard error in a future release!
[INFO] [stdout]     = note: for more information, see issue #147992 <https://github.com/rust-lang/rust/issues/147992>
[INFO] [stdout] 
[INFO] [stdout] 
[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: Use of ambiguously glob imported trait `Read`
[INFO] [stdout]    --> src/parse_files.rs:184:53
[INFO] [stdout]     |
[INFO] [stdout]   8 | use rust_htslib::bam::*;
[INFO] [stdout]     |     ---------------- `Read` imported ambiguously here
[INFO] [stdout] ...
[INFO] [stdout] 184 |     let mut header = bam::Header::from_template(bam.header());
[INFO] [stdout]     |                                                     ^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: Import `Read` explicitly
[INFO] [stdout]     = warning: this was previously accepted by the compiler but is being phased out; it will become a hard error in a future release!
[INFO] [stdout]     = note: for more information, see issue #147992 <https://github.com/rust-lang/rust/issues/147992>
[INFO] [stdout]     = note: `#[warn(ambiguous_glob_imported_traits)]` (part of `#[warn(future_incompatible)]`) 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: Use of ambiguously glob imported trait `Read`
[INFO] [stdout]    --> src/parse_files.rs:198:20
[INFO] [stdout]     |
[INFO] [stdout]   8 | use rust_htslib::bam::*;
[INFO] [stdout]     |     ---------------- `Read` imported ambiguously here
[INFO] [stdout] ...
[INFO] [stdout] 198 |     for rec in bam.records() {
[INFO] [stdout]     |                    ^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = help: Import `Read` explicitly
[INFO] [stdout]     = warning: this was previously accepted by the compiler but is being phased out; it will become a hard error in a future release!
[INFO] [stdout]     = note: for more information, see issue #147992 <https://github.com/rust-lang/rust/issues/147992>
[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] 372 |                     seq_len_from_cig += cigar.len();
[INFO] [stdout]     |                     ------------------------------- `seq_len_from_cig` is overwritten here before the previous value is read
[INFO] [stdout] 373 |                 } else if matches!(cigar, hts_Cigar::SoftClip(u32)) {
[INFO] [stdout] 374 |                     seq_len_from_cig += cigar.len();
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout]     |
[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] 369 |                     seq_len_from_cig += cigar.len();
[INFO] [stdout]     |                     ------------------------------- `seq_len_from_cig` is overwritten here before the previous value is read
[INFO] [stdout] ...
[INFO] [stdout] 372 |                     seq_len_from_cig += cigar.len();
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[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] [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] 372 |                     seq_len_from_cig += cigar.len();
[INFO] [stdout]     |                     ------------------------------- `seq_len_from_cig` is overwritten here before the previous value is read
[INFO] [stdout] 373 |                 } else if matches!(cigar, hts_Cigar::SoftClip(u32)) {
[INFO] [stdout] 374 |                     seq_len_from_cig += cigar.len();
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout]     |
[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] 369 |                     seq_len_from_cig += cigar.len();
[INFO] [stdout]     |                     ------------------------------- `seq_len_from_cig` is overwritten here before the previous value is read
[INFO] [stdout] ...
[INFO] [stdout] 372 |                     seq_len_from_cig += cigar.len();
[INFO] [stdout]     |                     ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ this value is reassigned later and never used
[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 2m 38s
[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 3`
[INFO] running `Command { std: "docker" "inspect" "ee4ac55a6509467db75ec465a8a581e7d7532091a3ddf9f671781ea7fe0105dc", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "ee4ac55a6509467db75ec465a8a581e7d7532091a3ddf9f671781ea7fe0105dc", kill_on_drop: false }`
[INFO] [stdout] ee4ac55a6509467db75ec465a8a581e7d7532091a3ddf9f671781ea7fe0105dc
