[INFO] cloning repository https://github.com/LooneyRichie/Instant-DNA
[INFO] running `Command { std: "git" "-c" "credential.helper=" "-c" "credential.helper=/workspace/cargo-home/bin/git-credential-null" "clone" "--bare" "https://github.com/LooneyRichie/Instant-DNA" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FLooneyRichie%2FInstant-DNA", kill_on_drop: false }`
[INFO] [stderr] Cloning into bare repository '/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FLooneyRichie%2FInstant-DNA'...
[INFO] running `Command { std: "git" "rev-parse" "HEAD", kill_on_drop: false }`
[INFO] [stdout] 0bfbf51790c6af7d5194c7dc86c28cfe0d650bfd
[INFO] checking LooneyRichie/Instant-DNA against master#f28ac764c36004fa6a6e098d15b4016a838c13c6 for pr-158320
[INFO] running `Command { std: "git" "clone" "/workspace/cache/git-repos/https%3A%2F%2Fgithub.com%2FLooneyRichie%2FInstant-DNA" "/workspace/builds/worker-0-tc1/source", kill_on_drop: false }`
[INFO] [stderr] Cloning into '/workspace/builds/worker-0-tc1/source'...
[INFO] [stderr] done.
[INFO] started tweaking git repo https://github.com/LooneyRichie/Instant-DNA
[INFO] finished tweaking git repo https://github.com/LooneyRichie/Instant-DNA
[INFO] tweaked toml for git repo https://github.com/LooneyRichie/Instant-DNA written to /workspace/builds/worker-0-tc1/source/Cargo.toml
[INFO] validating manifest of git repo https://github.com/LooneyRichie/Instant-DNA on toolchain f28ac764c36004fa6a6e098d15b4016a838c13c6
[INFO] running `Command { std: CARGO_HOME="/workspace/cargo-home" RUSTUP_HOME="/workspace/rustup-home" "/workspace/cargo-home/bin/cargo" "+f28ac764c36004fa6a6e098d15b4016a838c13c6" "metadata" "--manifest-path" "Cargo.toml" "--no-deps", kill_on_drop: false }`
[INFO] crate git repo https://github.com/LooneyRichie/Instant-DNA 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" "+f28ac764c36004fa6a6e098d15b4016a838c13c6" "fetch" "--manifest-path" "Cargo.toml", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "create" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/source:/opt/rustwide/workdir:ro,Z" "-v" "/var/lib/crater-agent-workspace/builds/worker-0-tc1/target:/opt/rustwide/target:rw,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" "-m" "1610612736" "--network" "none" "ghcr.io/rust-lang/crates-build-env/linux@sha256:3a6becf2bc8dde7f3fa57ede90e4f284e72d296796fc446bbb1e2c7cc0530151" "sleep" "infinity", kill_on_drop: false }`
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[INFO] running `Command { std: "docker" "start" "efdef87a15ba892f02a64eef4bb58db70bfdc1c843b60b8f24561bbb62867247", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-e" "CARGO_TARGET_DIR=/opt/rustwide/target" "-w" "/opt/rustwide/workdir" "--user" "0:0" "efdef87a15ba892f02a64eef4bb58db70bfdc1c843b60b8f24561bbb62867247" "/opt/rustwide/cargo-home/bin/cargo" "+f28ac764c36004fa6a6e098d15b4016a838c13c6" "metadata" "--no-deps" "--format-version=1", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "inspect" "efdef87a15ba892f02a64eef4bb58db70bfdc1c843b60b8f24561bbb62867247", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "exec" "-e" "SOURCE_DIR=/opt/rustwide/workdir" "-e" "CARGO_HOME=/opt/rustwide/cargo-home" "-e" "RUSTUP_HOME=/opt/rustwide/rustup-home" "-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" "-w" "/opt/rustwide/workdir" "--user" "0:0" "efdef87a15ba892f02a64eef4bb58db70bfdc1c843b60b8f24561bbb62867247" "/opt/rustwide/cargo-home/bin/cargo" "+f28ac764c36004fa6a6e098d15b4016a838c13c6" "check" "--frozen" "--all" "--all-targets" "--message-format=json", kill_on_drop: false }`
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[INFO] [stdout] warning: unused import: `std::collections::HashMap`
[INFO] [stdout]  --> src/main.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use std::collections::HashMap;
[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: `std::collections::HashMap`
[INFO] [stdout]  --> src/main.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use std::collections::HashMap;
[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: `Arc` and `Mutex`
[INFO] [stdout]  --> src/main.rs:4:17
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::sync::{Arc, Mutex};
[INFO] [stdout]   |                 ^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused imports: `Arc` and `Mutex`
[INFO] [stdout]  --> src/main.rs:4:17
[INFO] [stdout]   |
[INFO] [stdout] 4 | use std::sync::{Arc, Mutex};
[INFO] [stdout]   |                 ^^^  ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::path::Path`
[INFO] [stdout]  --> src/raw_converter.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use std::path::Path;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `std::path::Path`
[INFO] [stdout]  --> src/raw_converter.rs:3:5
[INFO] [stdout]   |
[INFO] [stdout] 3 | use std::path::Path;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debug`
[INFO] [stdout]  --> src/raw_converter.rs:6:23
[INFO] [stdout]   |
[INFO] [stdout] 6 | use log::{info, warn, debug};
[INFO] [stdout]   |                       ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `debug`
[INFO] [stdout]  --> src/raw_converter.rs:6:23
[INFO] [stdout]   |
[INFO] [stdout] 6 | use log::{info, warn, debug};
[INFO] [stdout]   |                       ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/main.rs:1:5
[INFO] [stdout]   |
[INFO] [stdout] 1 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused import: `rayon::prelude`
[INFO] [stdout]  --> src/main.rs:1:5
[INFO] [stdout]   |
[INFO] [stdout] 1 | use rayon::prelude::*;
[INFO] [stdout]   |     ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `sequences` is never read
[INFO] [stdout]   --> src/sequencer.rs:30:29
[INFO] [stdout]    |
[INFO] [stdout] 30 |         let mut sequences = Vec::new();
[INFO] [stdout]    |                             ^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 39 |             sequences = self.parse_auto_detect(input_path, optimizer)?;
[INFO] [stdout]    |             --------- `sequences` is overwritten here before the previous value is read
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]    --> src/sequencer.rs:167:9
[INFO] [stdout]     |
[INFO] [stdout] 167 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]     |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: value assigned to `sequences` is never read
[INFO] [stdout]   --> src/sequencer.rs:30:29
[INFO] [stdout]    |
[INFO] [stdout] 30 |         let mut sequences = Vec::new();
[INFO] [stdout]    |                             ^^^^^^^^^^ this value is reassigned later and never used
[INFO] [stdout] ...
[INFO] [stdout] 39 |             sequences = self.parse_auto_detect(input_path, optimizer)?;
[INFO] [stdout]    |             --------- `sequences` is overwritten here before the previous value is read
[INFO] [stdout]    |
[INFO] [stdout]    = note: `#[warn(unused_assignments)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]    --> src/binary_optimizer.rs:110:14
[INFO] [stdout]     |
[INFO] [stdout] 110 |         for (i, &byte) in compressed.iter().enumerate() {
[INFO] [stdout]     |              ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]    --> src/sequencer.rs:167:9
[INFO] [stdout]     |
[INFO] [stdout] 167 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]     |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(unused_variables)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_path`
[INFO] [stdout]   --> src/genetic_analyzer.rs:16:9
[INFO] [stdout]    |
[INFO] [stdout] 16 |         input_path: &str,
[INFO] [stdout]    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_path`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `analysis_type`
[INFO] [stdout]   --> src/genetic_analyzer.rs:17:9
[INFO] [stdout]    |
[INFO] [stdout] 17 |         analysis_type: &str,
[INFO] [stdout]    |         ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_analysis_type`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]   --> src/genetic_analyzer.rs:18:9
[INFO] [stdout]    |
[INFO] [stdout] 18 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]   --> src/genetic_analyzer.rs:45:9
[INFO] [stdout]    |
[INFO] [stdout] 45 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_path`
[INFO] [stdout]   --> src/rna_processor.rs:16:9
[INFO] [stdout]    |
[INFO] [stdout] 16 |         input_path: &str,
[INFO] [stdout]    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_path`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `analysis_type`
[INFO] [stdout]   --> src/rna_processor.rs:17:9
[INFO] [stdout]    |
[INFO] [stdout] 17 |         analysis_type: &str,
[INFO] [stdout]    |         ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_analysis_type`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `secondary_structure`
[INFO] [stdout]   --> src/rna_processor.rs:18:9
[INFO] [stdout]    |
[INFO] [stdout] 18 |         secondary_structure: bool,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_secondary_structure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]   --> src/rna_processor.rs:19:9
[INFO] [stdout]    |
[INFO] [stdout] 19 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `file1`
[INFO] [stdout]   --> src/alignment.rs:16:9
[INFO] [stdout]    |
[INFO] [stdout] 16 |         file1: &str,
[INFO] [stdout]    |         ^^^^^ help: if this is intentional, prefix it with an underscore: `_file1`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `file2`
[INFO] [stdout]   --> src/alignment.rs:17:9
[INFO] [stdout]    |
[INFO] [stdout] 17 |         file2: &str,
[INFO] [stdout]    |         ^^^^^ help: if this is intentional, prefix it with an underscore: `_file2`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `algorithm`
[INFO] [stdout]   --> src/alignment.rs:18:9
[INFO] [stdout]    |
[INFO] [stdout] 18 |         algorithm: &str,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_algorithm`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]   --> src/alignment.rs:19:9
[INFO] [stdout]    |
[INFO] [stdout] 19 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_path`
[INFO] [stdout]   --> src/variant_caller.rs:16:9
[INFO] [stdout]    |
[INFO] [stdout] 16 |         input_path: &str,
[INFO] [stdout]    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_path`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `reference`
[INFO] [stdout]   --> src/variant_caller.rs:17:9
[INFO] [stdout]    |
[INFO] [stdout] 17 |         reference: &str,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reference`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `variant_type`
[INFO] [stdout]   --> src/variant_caller.rs:18:9
[INFO] [stdout]    |
[INFO] [stdout] 18 |         variant_type: &str,
[INFO] [stdout]    |         ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_variant_type`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]   --> src/variant_caller.rs:19:9
[INFO] [stdout]    |
[INFO] [stdout] 19 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_path`
[INFO] [stdout]   --> src/assembly.rs:20:9
[INFO] [stdout]    |
[INFO] [stdout] 20 |         input_path: &str,
[INFO] [stdout]    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_path`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `algorithm`
[INFO] [stdout]   --> src/assembly.rs:21:9
[INFO] [stdout]    |
[INFO] [stdout] 21 |         algorithm: &str,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_algorithm`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]   --> src/assembly.rs:22:9
[INFO] [stdout]    |
[INFO] [stdout] 22 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `i`
[INFO] [stdout]    --> src/binary_optimizer.rs:110:14
[INFO] [stdout]     |
[INFO] [stdout] 110 |         for (i, &byte) in compressed.iter().enumerate() {
[INFO] [stdout]     |              ^ help: if this is intentional, prefix it with an underscore: `_i`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_path`
[INFO] [stdout]   --> src/genetic_analyzer.rs:16:9
[INFO] [stdout]    |
[INFO] [stdout] 16 |         input_path: &str,
[INFO] [stdout]    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_path`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `analysis_type`
[INFO] [stdout]   --> src/genetic_analyzer.rs:17:9
[INFO] [stdout]    |
[INFO] [stdout] 17 |         analysis_type: &str,
[INFO] [stdout]    |         ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_analysis_type`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]   --> src/genetic_analyzer.rs:18:9
[INFO] [stdout]    |
[INFO] [stdout] 18 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `gender`
[INFO] [stdout]    --> src/vcf_processor.rs:117:21
[INFO] [stdout]     |
[INFO] [stdout] 117 |                 let gender = parts[3].to_string();
[INFO] [stdout]     |                     ^^^^^^ help: if this is intentional, prefix it with an underscore: `_gender`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]   --> src/genetic_analyzer.rs:45:9
[INFO] [stdout]    |
[INFO] [stdout] 45 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_path`
[INFO] [stdout]   --> src/rna_processor.rs:16:9
[INFO] [stdout]    |
[INFO] [stdout] 16 |         input_path: &str,
[INFO] [stdout]    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_path`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `analysis_type`
[INFO] [stdout]   --> src/rna_processor.rs:17:9
[INFO] [stdout]    |
[INFO] [stdout] 17 |         analysis_type: &str,
[INFO] [stdout]    |         ^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_analysis_type`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `secondary_structure`
[INFO] [stdout]   --> src/rna_processor.rs:18:9
[INFO] [stdout]    |
[INFO] [stdout] 18 |         secondary_structure: bool,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_secondary_structure`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]   --> src/rna_processor.rs:19:9
[INFO] [stdout]    |
[INFO] [stdout] 19 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `file1`
[INFO] [stdout]   --> src/alignment.rs:16:9
[INFO] [stdout]    |
[INFO] [stdout] 16 |         file1: &str,
[INFO] [stdout]    |         ^^^^^ help: if this is intentional, prefix it with an underscore: `_file1`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `file2`
[INFO] [stdout]   --> src/alignment.rs:17:9
[INFO] [stdout]    |
[INFO] [stdout] 17 |         file2: &str,
[INFO] [stdout]    |         ^^^^^ help: if this is intentional, prefix it with an underscore: `_file2`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `algorithm`
[INFO] [stdout]   --> src/alignment.rs:18:9
[INFO] [stdout]    |
[INFO] [stdout] 18 |         algorithm: &str,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_algorithm`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]   --> src/alignment.rs:19:9
[INFO] [stdout]    |
[INFO] [stdout] 19 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_path`
[INFO] [stdout]   --> src/variant_caller.rs:16:9
[INFO] [stdout]    |
[INFO] [stdout] 16 |         input_path: &str,
[INFO] [stdout]    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_path`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `reference`
[INFO] [stdout]   --> src/variant_caller.rs:17:9
[INFO] [stdout]    |
[INFO] [stdout] 17 |         reference: &str,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_reference`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `variant_type`
[INFO] [stdout]   --> src/variant_caller.rs:18:9
[INFO] [stdout]    |
[INFO] [stdout] 18 |         variant_type: &str,
[INFO] [stdout]    |         ^^^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_variant_type`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]   --> src/variant_caller.rs:19:9
[INFO] [stdout]    |
[INFO] [stdout] 19 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `input_path`
[INFO] [stdout]   --> src/assembly.rs:20:9
[INFO] [stdout]    |
[INFO] [stdout] 20 |         input_path: &str,
[INFO] [stdout]    |         ^^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_input_path`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `algorithm`
[INFO] [stdout]   --> src/assembly.rs:21:9
[INFO] [stdout]    |
[INFO] [stdout] 21 |         algorithm: &str,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_algorithm`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `optimizer`
[INFO] [stdout]   --> src/assembly.rs:22:9
[INFO] [stdout]    |
[INFO] [stdout] 22 |         optimizer: &BinaryOptimizer,
[INFO] [stdout]    |         ^^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_optimizer`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `pop_code`
[INFO] [stdout]    --> src/vcf_processor.rs:228:18
[INFO] [stdout]     |
[INFO] [stdout] 228 |             for (pop_code, population) in &self.populations {
[INFO] [stdout]     |                  ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_pop_code`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `gender`
[INFO] [stdout]    --> src/vcf_processor.rs:117:21
[INFO] [stdout]     |
[INFO] [stdout] 117 |                 let gender = parts[3].to_string();
[INFO] [stdout]     |                     ^^^^^^ help: if this is intentional, prefix it with an underscore: `_gender`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: unused variable: `pop_code`
[INFO] [stdout]    --> src/vcf_processor.rs:228:18
[INFO] [stdout]     |
[INFO] [stdout] 228 |             for (pop_code, population) in &self.populations {
[INFO] [stdout]     |                  ^^^^^^^^ help: if this is intentional, prefix it with an underscore: `_pop_code`
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `AnalysisResult` is never constructed
[INFO] [stdout]    --> src/main.rs:349:8
[INFO] [stdout]     |
[INFO] [stdout] 349 | struct AnalysisResult {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `simd_enabled` and `cache` are never read
[INFO] [stdout]  --> src/dna_engine.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | pub struct DnaEngine {
[INFO] [stdout]   |            --------- fields in this struct
[INFO] [stdout] 8 |     simd_enabled: bool,
[INFO] [stdout]   |     ^^^^^^^^^^^^
[INFO] [stdout] 9 |     cache: Arc<AHashMap<String, Vec<u8>>>,
[INFO] [stdout]   |     ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: multiple methods are never used
[INFO] [stdout]    --> src/dna_engine.rs:20:12
[INFO] [stdout]     |
[INFO] [stdout]  12 | impl DnaEngine {
[INFO] [stdout]     | -------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout]  20 |     pub fn has_simd_support(&self) -> bool {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  25 |     pub fn sequence_to_binary(&self, sequence: &str) -> Vec<u8> {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  39 |     pub fn binary_to_sequence(&self, binary: &[u8]) -> String {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  53 |     pub fn analyze_parallel(&self, sequences: &[String]) -> Result<Vec<AnalysisResult>> {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  62 |     fn analyze_sequence(&self, sequence: &str) -> Result<AnalysisResult> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  78 |     fn calculate_gc_content(&self, binary_seq: &[u8]) -> f64 {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  86 |     fn calculate_complexity(&self, binary_seq: &[u8]) -> f64 {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 106 |     fn find_repeats(&self, binary_seq: &[u8]) -> Vec<RepeatRegion> {
[INFO] [stdout]     |        ^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 136 |     fn generate_binary_signature(&self, binary_seq: &[u8]) -> Vec<u8> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `AnalysisResult` is never constructed
[INFO] [stdout]    --> src/dna_engine.rs:150:12
[INFO] [stdout]     |
[INFO] [stdout] 150 | pub struct AnalysisResult {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `RepeatRegion` is never constructed
[INFO] [stdout]    --> src/dna_engine.rs:159:12
[INFO] [stdout]     |
[INFO] [stdout] 159 | pub struct RepeatRegion {
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `Sequencer` is never constructed
[INFO] [stdout]  --> src/sequencer.rs:7:12
[INFO] [stdout]   |
[INFO] [stdout] 7 | pub struct Sequencer {
[INFO] [stdout]   |            ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: multiple associated items are never used
[INFO] [stdout]    --> src/sequencer.rs:14:12
[INFO] [stdout]     |
[INFO] [stdout]  13 | impl Sequencer {
[INFO] [stdout]     | -------------- associated items in this implementation
[INFO] [stdout]  14 |     pub fn new(quality_threshold: u8, max_read_length: usize) -> Result<Self> {
[INFO] [stdout]     |            ^^^
[INFO] [stdout] ...
[INFO] [stdout]  22 |     pub fn enable_realtime(&mut self) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  27 |     pub fn process_file(&self, input_path: &str, optimizer: &BinaryOptimizer) -> Result<Vec<SequenceData>> {
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  51 |     fn parse_fasta(&self, reader: BufReader<File>, optimizer: &BinaryOptimizer) -> Result<Vec<SequenceData>> {
[INFO] [stdout]     |        ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  91 |     fn parse_fastq(&self, reader: BufReader<File>, optimizer: &BinaryOptimizer) -> Result<Vec<SequenceData>> {
[INFO] [stdout]     |        ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 121 |     fn parse_auto_detect(&self, input_path: &str, optimizer: &BinaryOptimizer) -> Result<Vec<SequenceData>> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 142 |     fn parse_raw_dna(&self, reader: BufReader<File>, optimizer: &BinaryOptimizer) -> Result<Vec<SequenceData>> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 162 |     fn create_sequence_data(
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `SequenceData` is never constructed
[INFO] [stdout]    --> src/sequencer.rs:195:12
[INFO] [stdout]     |
[INFO] [stdout] 195 | pub struct SequenceData {
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `avg_quality`, `gc_content`, and `length` are never used
[INFO] [stdout]    --> src/sequencer.rs:204:12
[INFO] [stdout]     |
[INFO] [stdout] 203 | impl SequenceData {
[INFO] [stdout]     | ----------------- methods in this implementation
[INFO] [stdout] 204 |     pub fn avg_quality(&self) -> f64 {
[INFO] [stdout]     |            ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 213 |     pub fn gc_content(&self) -> f64 {
[INFO] [stdout]     |            ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 221 |     pub fn length(&self) -> usize {
[INFO] [stdout]     |            ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `QualityScore` is never constructed
[INFO] [stdout]    --> src/sequencer.rs:227:12
[INFO] [stdout]     |
[INFO] [stdout] 227 | pub struct QualityScore;
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated functions `phred_to_probability` and `probability_to_phred` are never used
[INFO] [stdout]    --> src/sequencer.rs:230:12
[INFO] [stdout]     |
[INFO] [stdout] 229 | impl QualityScore {
[INFO] [stdout]     | ----------------- associated functions in this implementation
[INFO] [stdout] 230 |     pub fn phred_to_probability(phred: u8) -> f64 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 234 |     pub fn probability_to_phred(prob: f64) -> u8 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `simd_enabled` is never read
[INFO] [stdout]  --> src/binary_optimizer.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | pub struct BinaryOptimizer {
[INFO] [stdout]   |            --------------- field in this struct
[INFO] [stdout] 5 |     simd_enabled: bool,
[INFO] [stdout]   |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: multiple methods are never used
[INFO] [stdout]    --> src/binary_optimizer.rs:21:12
[INFO] [stdout]     |
[INFO] [stdout]   8 | impl BinaryOptimizer {
[INFO] [stdout]     | -------------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout]  21 |     pub fn find_pattern(&self, sequence: &[u8], pattern: &[u8]) -> Vec<usize> {
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  29 |     fn simd_pattern_search(&self, sequence: &[u8], pattern: &[u8]) -> Vec<usize> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  46 |     fn scalar_pattern_search(&self, sequence: &[u8], pattern: &[u8]) -> Vec<usize> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  59 |     pub fn compare_sequences(&self, seq1: &[u8], seq2: &[u8]) -> f64 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  74 |     pub fn count_kmers(&self, sequence: &[u8], k: usize) -> ahash::AHashMap<Vec<u8>, u32> {
[INFO] [stdout]     |            ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  91 |     pub fn compress_sequence(&self, sequence: &[u8]) -> Vec<u8> {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 107 |     pub fn decompress_sequence(&self, compressed: &[u8], original_length: usize) -> Vec<u8> {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `SimdProcessor` is never constructed
[INFO] [stdout]    --> src/binary_optimizer.rs:126:12
[INFO] [stdout]     |
[INFO] [stdout] 126 | pub struct SimdProcessor;
[INFO] [stdout]     |            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated functions `new`, `count_bases_simd`, and `analyze_quality_simd` are never used
[INFO] [stdout]    --> src/binary_optimizer.rs:129:12
[INFO] [stdout]     |
[INFO] [stdout] 128 | impl SimdProcessor {
[INFO] [stdout]     | ------------------ associated functions in this implementation
[INFO] [stdout] 129 |     pub fn new() -> Self {
[INFO] [stdout]     |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 134 |     pub fn count_bases_simd(sequence: &[u8]) -> [u32; 4] {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 148 |     pub fn analyze_quality_simd(quality_scores: &[u8]) -> QualityStats {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `QualityStats` is never constructed
[INFO] [stdout]    --> src/binary_optimizer.rs:163:12
[INFO] [stdout]     |
[INFO] [stdout] 163 | pub struct QualityStats {
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `GeneticAnalyzer` is never constructed
[INFO] [stdout]  --> src/genetic_analyzer.rs:5:12
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub struct GeneticAnalyzer {
[INFO] [stdout]   |            ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `new`, `analyze_file`, and `benchmark_analysis` are never used
[INFO] [stdout]   --> src/genetic_analyzer.rs:10:12
[INFO] [stdout]    |
[INFO] [stdout]  9 | impl GeneticAnalyzer {
[INFO] [stdout]    | -------------------- associated items in this implementation
[INFO] [stdout] 10 |     pub fn new(deep_analysis: bool) -> Result<Self> {
[INFO] [stdout]    |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 14 |     pub fn analyze_file(
[INFO] [stdout]    |            ^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 42 |     pub fn benchmark_analysis(
[INFO] [stdout]    |            ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `RnaProcessor` is never constructed
[INFO] [stdout]  --> src/rna_processor.rs:5:12
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub struct RnaProcessor {
[INFO] [stdout]   |            ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `new` and `analyze` are never used
[INFO] [stdout]   --> src/rna_processor.rs:10:12
[INFO] [stdout]    |
[INFO] [stdout]  9 | impl RnaProcessor {
[INFO] [stdout]    | ----------------- associated items in this implementation
[INFO] [stdout] 10 |     pub fn new(temperature: f64) -> Result<Self> {
[INFO] [stdout]    |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 14 |     pub fn analyze(
[INFO] [stdout]    |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `RnaAnalysisResult` is never constructed
[INFO] [stdout]   --> src/rna_processor.rs:32:12
[INFO] [stdout]    |
[INFO] [stdout] 32 | pub struct RnaAnalysisResult {
[INFO] [stdout]    |            ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `AlignmentEngine` is never constructed
[INFO] [stdout]  --> src/alignment.rs:5:12
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub struct AlignmentEngine {
[INFO] [stdout]   |            ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `new` and `compare_files` are never used
[INFO] [stdout]   --> src/alignment.rs:10:12
[INFO] [stdout]    |
[INFO] [stdout]  9 | impl AlignmentEngine {
[INFO] [stdout]    | -------------------- associated items in this implementation
[INFO] [stdout] 10 |     pub fn new(binary_optimized: bool) -> Result<Self> {
[INFO] [stdout]    |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 14 |     pub fn compare_files(
[INFO] [stdout]    |            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `VariantCaller` is never constructed
[INFO] [stdout]  --> src/variant_caller.rs:5:12
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub struct VariantCaller {
[INFO] [stdout]   |            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `new` and `call_variants` are never used
[INFO] [stdout]   --> src/variant_caller.rs:10:12
[INFO] [stdout]    |
[INFO] [stdout]  9 | impl VariantCaller {
[INFO] [stdout]    | ------------------ associated items in this implementation
[INFO] [stdout] 10 |     pub fn new(min_coverage: u32) -> Result<Self> {
[INFO] [stdout]    |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 14 |     pub fn call_variants(
[INFO] [stdout]    |            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `AssemblyEngine` is never constructed
[INFO] [stdout]  --> src/assembly.rs:5:12
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub struct AssemblyEngine {
[INFO] [stdout]   |            ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `new` and `assemble` are never used
[INFO] [stdout]   --> src/assembly.rs:11:12
[INFO] [stdout]    |
[INFO] [stdout] 10 | impl AssemblyEngine {
[INFO] [stdout]    | ------------------- associated items in this implementation
[INFO] [stdout] 11 |     pub fn new(kmer_size: usize, error_correction: bool) -> Result<Self> {
[INFO] [stdout]    |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 18 |     pub fn assemble(
[INFO] [stdout]    |            ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `position` and `quality` are never read
[INFO] [stdout]   --> src/vcf_processor.rs:11:9
[INFO] [stdout]    |
[INFO] [stdout]  9 | pub struct SNPVariant {
[INFO] [stdout]    |            ---------- fields in this struct
[INFO] [stdout] 10 |     pub chromosome: String,
[INFO] [stdout] 11 |     pub position: u64,
[INFO] [stdout]    |         ^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 15 |     pub quality: f64,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `SNPVariant` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `region` is never read
[INFO] [stdout]   --> src/vcf_processor.rs:24:9
[INFO] [stdout]    |
[INFO] [stdout] 20 | pub struct Population {
[INFO] [stdout]    |            ---------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 24 |     pub region: String,
[INFO] [stdout]    |         ^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `Population` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `memory_mb` and `cpu_percent` are never read
[INFO] [stdout]   --> src/benchmark.rs:13:9
[INFO] [stdout]    |
[INFO] [stdout]  8 | pub struct BenchmarkResult {
[INFO] [stdout]    |            --------------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 13 |     pub memory_mb: f64,
[INFO] [stdout]    |         ^^^^^^^^^
[INFO] [stdout] 14 |     pub cpu_percent: f64,
[INFO] [stdout]    |         ^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `BenchmarkResult` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `reference` and `alternate` are never read
[INFO] [stdout]   --> src/raw_converter.rs:35:9
[INFO] [stdout]    |
[INFO] [stdout] 30 | pub struct SnpData {
[INFO] [stdout]    |            ------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 35 |     pub reference: Option<String>,
[INFO] [stdout]    |         ^^^^^^^^^
[INFO] [stdout] 36 |     pub alternate: Option<String>,
[INFO] [stdout]    |         ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `SnpData` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `output_compression` is never read
[INFO] [stdout]   --> src/raw_converter.rs:43:9
[INFO] [stdout]    |
[INFO] [stdout] 40 | pub struct RawDnaConverter {
[INFO] [stdout]    |            --------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 43 |     pub output_compression: bool,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `RawDnaConverter` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `extraction_method` is never read
[INFO] [stdout]   --> src/diy_dna.rs:19:9
[INFO] [stdout]    |
[INFO] [stdout] 17 | pub struct DiyDnaExtractor {
[INFO] [stdout]    |            --------------- field in this struct
[INFO] [stdout] 18 |     pub sample_name: String,
[INFO] [stdout] 19 |     pub extraction_method: String,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `DiyDnaExtractor` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `AnalysisResult` is never constructed
[INFO] [stdout]    --> src/main.rs:349:8
[INFO] [stdout]     |
[INFO] [stdout] 349 | struct AnalysisResult {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^
[INFO] [stdout]     |
[INFO] [stdout]     = note: `#[warn(dead_code)]` (part of `#[warn(unused)]`) on by default
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `simd_enabled` and `cache` are never read
[INFO] [stdout]  --> src/dna_engine.rs:8:5
[INFO] [stdout]   |
[INFO] [stdout] 7 | pub struct DnaEngine {
[INFO] [stdout]   |            --------- fields in this struct
[INFO] [stdout] 8 |     simd_enabled: bool,
[INFO] [stdout]   |     ^^^^^^^^^^^^
[INFO] [stdout] 9 |     cache: Arc<AHashMap<String, Vec<u8>>>,
[INFO] [stdout]   |     ^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: multiple methods are never used
[INFO] [stdout]    --> src/dna_engine.rs:20:12
[INFO] [stdout]     |
[INFO] [stdout]  12 | impl DnaEngine {
[INFO] [stdout]     | -------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout]  20 |     pub fn has_simd_support(&self) -> bool {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  25 |     pub fn sequence_to_binary(&self, sequence: &str) -> Vec<u8> {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  39 |     pub fn binary_to_sequence(&self, binary: &[u8]) -> String {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  53 |     pub fn analyze_parallel(&self, sequences: &[String]) -> Result<Vec<AnalysisResult>> {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  62 |     fn analyze_sequence(&self, sequence: &str) -> Result<AnalysisResult> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  78 |     fn calculate_gc_content(&self, binary_seq: &[u8]) -> f64 {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  86 |     fn calculate_complexity(&self, binary_seq: &[u8]) -> f64 {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 106 |     fn find_repeats(&self, binary_seq: &[u8]) -> Vec<RepeatRegion> {
[INFO] [stdout]     |        ^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 136 |     fn generate_binary_signature(&self, binary_seq: &[u8]) -> Vec<u8> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `AnalysisResult` is never constructed
[INFO] [stdout]    --> src/dna_engine.rs:150:12
[INFO] [stdout]     |
[INFO] [stdout] 150 | pub struct AnalysisResult {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `RepeatRegion` is never constructed
[INFO] [stdout]    --> src/dna_engine.rs:159:12
[INFO] [stdout]     |
[INFO] [stdout] 159 | pub struct RepeatRegion {
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `Sequencer` is never constructed
[INFO] [stdout]  --> src/sequencer.rs:7:12
[INFO] [stdout]   |
[INFO] [stdout] 7 | pub struct Sequencer {
[INFO] [stdout]   |            ^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: multiple associated items are never used
[INFO] [stdout]    --> src/sequencer.rs:14:12
[INFO] [stdout]     |
[INFO] [stdout]  13 | impl Sequencer {
[INFO] [stdout]     | -------------- associated items in this implementation
[INFO] [stdout]  14 |     pub fn new(quality_threshold: u8, max_read_length: usize) -> Result<Self> {
[INFO] [stdout]     |            ^^^
[INFO] [stdout] ...
[INFO] [stdout]  22 |     pub fn enable_realtime(&mut self) {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  27 |     pub fn process_file(&self, input_path: &str, optimizer: &BinaryOptimizer) -> Result<Vec<SequenceData>> {
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  51 |     fn parse_fasta(&self, reader: BufReader<File>, optimizer: &BinaryOptimizer) -> Result<Vec<SequenceData>> {
[INFO] [stdout]     |        ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  91 |     fn parse_fastq(&self, reader: BufReader<File>, optimizer: &BinaryOptimizer) -> Result<Vec<SequenceData>> {
[INFO] [stdout]     |        ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 121 |     fn parse_auto_detect(&self, input_path: &str, optimizer: &BinaryOptimizer) -> Result<Vec<SequenceData>> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 142 |     fn parse_raw_dna(&self, reader: BufReader<File>, optimizer: &BinaryOptimizer) -> Result<Vec<SequenceData>> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 162 |     fn create_sequence_data(
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `SequenceData` is never constructed
[INFO] [stdout]    --> src/sequencer.rs:195:12
[INFO] [stdout]     |
[INFO] [stdout] 195 | pub struct SequenceData {
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: methods `avg_quality`, `gc_content`, and `length` are never used
[INFO] [stdout]    --> src/sequencer.rs:204:12
[INFO] [stdout]     |
[INFO] [stdout] 203 | impl SequenceData {
[INFO] [stdout]     | ----------------- methods in this implementation
[INFO] [stdout] 204 |     pub fn avg_quality(&self) -> f64 {
[INFO] [stdout]     |            ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 213 |     pub fn gc_content(&self) -> f64 {
[INFO] [stdout]     |            ^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 221 |     pub fn length(&self) -> usize {
[INFO] [stdout]     |            ^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `QualityScore` is never constructed
[INFO] [stdout]    --> src/sequencer.rs:227:12
[INFO] [stdout]     |
[INFO] [stdout] 227 | pub struct QualityScore;
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated functions `phred_to_probability` and `probability_to_phred` are never used
[INFO] [stdout]    --> src/sequencer.rs:230:12
[INFO] [stdout]     |
[INFO] [stdout] 229 | impl QualityScore {
[INFO] [stdout]     | ----------------- associated functions in this implementation
[INFO] [stdout] 230 |     pub fn phred_to_probability(phred: u8) -> f64 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 234 |     pub fn probability_to_phred(prob: f64) -> u8 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `simd_enabled` is never read
[INFO] [stdout]  --> src/binary_optimizer.rs:5:5
[INFO] [stdout]   |
[INFO] [stdout] 4 | pub struct BinaryOptimizer {
[INFO] [stdout]   |            --------------- field in this struct
[INFO] [stdout] 5 |     simd_enabled: bool,
[INFO] [stdout]   |     ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: multiple methods are never used
[INFO] [stdout]    --> src/binary_optimizer.rs:21:12
[INFO] [stdout]     |
[INFO] [stdout]   8 | impl BinaryOptimizer {
[INFO] [stdout]     | -------------------- methods in this implementation
[INFO] [stdout] ...
[INFO] [stdout]  21 |     pub fn find_pattern(&self, sequence: &[u8], pattern: &[u8]) -> Vec<usize> {
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  29 |     fn simd_pattern_search(&self, sequence: &[u8], pattern: &[u8]) -> Vec<usize> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  46 |     fn scalar_pattern_search(&self, sequence: &[u8], pattern: &[u8]) -> Vec<usize> {
[INFO] [stdout]     |        ^^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  59 |     pub fn compare_sequences(&self, seq1: &[u8], seq2: &[u8]) -> f64 {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  74 |     pub fn count_kmers(&self, sequence: &[u8], k: usize) -> ahash::AHashMap<Vec<u8>, u32> {
[INFO] [stdout]     |            ^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout]  91 |     pub fn compress_sequence(&self, sequence: &[u8]) -> Vec<u8> {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 107 |     pub fn decompress_sequence(&self, compressed: &[u8], original_length: usize) -> Vec<u8> {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `SimdProcessor` is never constructed
[INFO] [stdout]    --> src/binary_optimizer.rs:126:12
[INFO] [stdout]     |
[INFO] [stdout] 126 | pub struct SimdProcessor;
[INFO] [stdout]     |            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated functions `new`, `count_bases_simd`, and `analyze_quality_simd` are never used
[INFO] [stdout]    --> src/binary_optimizer.rs:129:12
[INFO] [stdout]     |
[INFO] [stdout] 128 | impl SimdProcessor {
[INFO] [stdout]     | ------------------ associated functions in this implementation
[INFO] [stdout] 129 |     pub fn new() -> Self {
[INFO] [stdout]     |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 134 |     pub fn count_bases_simd(sequence: &[u8]) -> [u32; 4] {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 148 |     pub fn analyze_quality_simd(quality_scores: &[u8]) -> QualityStats {
[INFO] [stdout]     |            ^^^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `QualityStats` is never constructed
[INFO] [stdout]    --> src/binary_optimizer.rs:163:12
[INFO] [stdout]     |
[INFO] [stdout] 163 | pub struct QualityStats {
[INFO] [stdout]     |            ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `GeneticAnalyzer` is never constructed
[INFO] [stdout]  --> src/genetic_analyzer.rs:5:12
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub struct GeneticAnalyzer {
[INFO] [stdout]   |            ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `new`, `analyze_file`, and `benchmark_analysis` are never used
[INFO] [stdout]   --> src/genetic_analyzer.rs:10:12
[INFO] [stdout]    |
[INFO] [stdout]  9 | impl GeneticAnalyzer {
[INFO] [stdout]    | -------------------- associated items in this implementation
[INFO] [stdout] 10 |     pub fn new(deep_analysis: bool) -> Result<Self> {
[INFO] [stdout]    |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 14 |     pub fn analyze_file(
[INFO] [stdout]    |            ^^^^^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 42 |     pub fn benchmark_analysis(
[INFO] [stdout]    |            ^^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `RnaProcessor` is never constructed
[INFO] [stdout]  --> src/rna_processor.rs:5:12
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub struct RnaProcessor {
[INFO] [stdout]   |            ^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `new` and `analyze` are never used
[INFO] [stdout]   --> src/rna_processor.rs:10:12
[INFO] [stdout]    |
[INFO] [stdout]  9 | impl RnaProcessor {
[INFO] [stdout]    | ----------------- associated items in this implementation
[INFO] [stdout] 10 |     pub fn new(temperature: f64) -> Result<Self> {
[INFO] [stdout]    |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 14 |     pub fn analyze(
[INFO] [stdout]    |            ^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `RnaAnalysisResult` is never constructed
[INFO] [stdout]   --> src/rna_processor.rs:32:12
[INFO] [stdout]    |
[INFO] [stdout] 32 | pub struct RnaAnalysisResult {
[INFO] [stdout]    |            ^^^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `AlignmentEngine` is never constructed
[INFO] [stdout]  --> src/alignment.rs:5:12
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub struct AlignmentEngine {
[INFO] [stdout]   |            ^^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `new` and `compare_files` are never used
[INFO] [stdout]   --> src/alignment.rs:10:12
[INFO] [stdout]    |
[INFO] [stdout]  9 | impl AlignmentEngine {
[INFO] [stdout]    | -------------------- associated items in this implementation
[INFO] [stdout] 10 |     pub fn new(binary_optimized: bool) -> Result<Self> {
[INFO] [stdout]    |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 14 |     pub fn compare_files(
[INFO] [stdout]    |            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `VariantCaller` is never constructed
[INFO] [stdout]  --> src/variant_caller.rs:5:12
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub struct VariantCaller {
[INFO] [stdout]   |            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `new` and `call_variants` are never used
[INFO] [stdout]   --> src/variant_caller.rs:10:12
[INFO] [stdout]    |
[INFO] [stdout]  9 | impl VariantCaller {
[INFO] [stdout]    | ------------------ associated items in this implementation
[INFO] [stdout] 10 |     pub fn new(min_coverage: u32) -> Result<Self> {
[INFO] [stdout]    |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 14 |     pub fn call_variants(
[INFO] [stdout]    |            ^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: struct `AssemblyEngine` is never constructed
[INFO] [stdout]  --> src/assembly.rs:5:12
[INFO] [stdout]   |
[INFO] [stdout] 5 | pub struct AssemblyEngine {
[INFO] [stdout]   |            ^^^^^^^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: associated items `new` and `assemble` are never used
[INFO] [stdout]   --> src/assembly.rs:11:12
[INFO] [stdout]    |
[INFO] [stdout] 10 | impl AssemblyEngine {
[INFO] [stdout]    | ------------------- associated items in this implementation
[INFO] [stdout] 11 |     pub fn new(kmer_size: usize, error_correction: bool) -> Result<Self> {
[INFO] [stdout]    |            ^^^
[INFO] [stdout] ...
[INFO] [stdout] 18 |     pub fn assemble(
[INFO] [stdout]    |            ^^^^^^^^
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `position` and `quality` are never read
[INFO] [stdout]   --> src/vcf_processor.rs:11:9
[INFO] [stdout]    |
[INFO] [stdout]  9 | pub struct SNPVariant {
[INFO] [stdout]    |            ---------- fields in this struct
[INFO] [stdout] 10 |     pub chromosome: String,
[INFO] [stdout] 11 |     pub position: u64,
[INFO] [stdout]    |         ^^^^^^^^
[INFO] [stdout] ...
[INFO] [stdout] 15 |     pub quality: f64,
[INFO] [stdout]    |         ^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `SNPVariant` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `region` is never read
[INFO] [stdout]   --> src/vcf_processor.rs:24:9
[INFO] [stdout]    |
[INFO] [stdout] 20 | pub struct Population {
[INFO] [stdout]    |            ---------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 24 |     pub region: String,
[INFO] [stdout]    |         ^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `Population` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `memory_mb` and `cpu_percent` are never read
[INFO] [stdout]   --> src/benchmark.rs:13:9
[INFO] [stdout]    |
[INFO] [stdout]  8 | pub struct BenchmarkResult {
[INFO] [stdout]    |            --------------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 13 |     pub memory_mb: f64,
[INFO] [stdout]    |         ^^^^^^^^^
[INFO] [stdout] 14 |     pub cpu_percent: f64,
[INFO] [stdout]    |         ^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `BenchmarkResult` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: fields `reference` and `alternate` are never read
[INFO] [stdout]   --> src/raw_converter.rs:35:9
[INFO] [stdout]    |
[INFO] [stdout] 30 | pub struct SnpData {
[INFO] [stdout]    |            ------- fields in this struct
[INFO] [stdout] ...
[INFO] [stdout] 35 |     pub reference: Option<String>,
[INFO] [stdout]    |         ^^^^^^^^^
[INFO] [stdout] 36 |     pub alternate: Option<String>,
[INFO] [stdout]    |         ^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `SnpData` has derived impls for the traits `Clone` and `Debug`, but these are intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `output_compression` is never read
[INFO] [stdout]   --> src/raw_converter.rs:43:9
[INFO] [stdout]    |
[INFO] [stdout] 40 | pub struct RawDnaConverter {
[INFO] [stdout]    |            --------------- field in this struct
[INFO] [stdout] ...
[INFO] [stdout] 43 |     pub output_compression: bool,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `RawDnaConverter` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stdout] warning: field `extraction_method` is never read
[INFO] [stdout]   --> src/diy_dna.rs:19:9
[INFO] [stdout]    |
[INFO] [stdout] 17 | pub struct DiyDnaExtractor {
[INFO] [stdout]    |            --------------- field in this struct
[INFO] [stdout] 18 |     pub sample_name: String,
[INFO] [stdout] 19 |     pub extraction_method: String,
[INFO] [stdout]    |         ^^^^^^^^^^^^^^^^^
[INFO] [stdout]    |
[INFO] [stdout]    = note: `DiyDnaExtractor` has a derived impl for the trait `Debug`, but this is intentionally ignored during dead code analysis
[INFO] [stdout] 
[INFO] [stdout] 
[INFO] [stderr]     Finished `dev` profile [optimized + debuginfo] target(s) in 6m 42s
[INFO] running `Command { std: "docker" "inspect" "efdef87a15ba892f02a64eef4bb58db70bfdc1c843b60b8f24561bbb62867247", kill_on_drop: false }`
[INFO] running `Command { std: "docker" "rm" "-f" "efdef87a15ba892f02a64eef4bb58db70bfdc1c843b60b8f24561bbb62867247", kill_on_drop: false }`
[INFO] [stdout] efdef87a15ba892f02a64eef4bb58db70bfdc1c843b60b8f24561bbb62867247
