fix: improper shuffling of records with same position in aln subcommand #79
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The random_sort function was only introducing randomness at the comparison level rather than properly shuffling groups of records with the same position. This meant that records with identical positions would maintain their original relative order instead of being randomly distributed within their group. Changes: - Replace random_sort/random_compare with shuffle_records_by_position - Group records by position before shuffling within each group - Add comprehensive tests including edge cases and regression tests - Fix clippy format string warnings in alignment.rs, fastx.rs, and subsampler.rs - Add demonstration test that reproduces the original bug The new implementation ensures that records with the same genomic position are properly randomized while maintaining correct positional ordering between different positions, fixing the reproducible bias in subsampling results. Fixes #76
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Pull Request Overview
This PR fixes a bug in the alignment subcommand where records with the same genomic position were not being properly randomized during subsampling. The random_sort function only introduced randomness at the comparison level rather than properly shuffling groups of records with identical positions, leading to reproducible bias in subsampling results.
- Replace flawed random_sort implementation with proper group-based shuffling
- Add comprehensive test coverage including regression tests that demonstrate the original bug
- Fix clippy format string warnings across multiple files
Reviewed Changes
Copilot reviewed 5 out of 5 changed files in this pull request and generated 1 comment.
Show a summary per file
| File | Description |
|---|---|
| src/alignment.rs | Core fix: replaces random_sort with shuffle_records_by_position and adds extensive tests |
| src/subsampler.rs | Updates println! format string to use newer syntax |
| src/reads.rs | Fixes format string in error message |
| src/fastx.rs | Updates Error::new to use Error::other method |
| src/cli.rs | Updates multiple format strings to use newer syntax |
Comments suppressed due to low confidence (4)
src/alignment.rs:691
- [nitpick] Test contains println! statements that will clutter test output. Consider using debug assertions or removing these print statements for cleaner test execution.
println!("Original order: {original_names:?}");
src/alignment.rs:798
- [nitpick] Test contains println! statements that will clutter test output. Consider using debug assertions or removing these print statements for cleaner test execution.
println!(
src/alignment.rs:878
- [nitpick] Test contains println! statements that will clutter test output. Consider using debug assertions or removing these print statements for cleaner test execution.
println!("Old approach: {same_order_count} out of 20 iterations kept the same order");
src/alignment.rs:892
- [nitpick] Test contains println! statements that will clutter test output. Consider using debug assertions or removing these print statements for cleaner test execution.
println!("New approach: {new_same_order_count} out of 20 iterations kept the same order");
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The random_sort function was only introducing randomness at the comparison level rather than properly shuffling groups of records with the same position. This meant that records with identical positions would maintain their original relative order instead of being randomly distributed within their group.
Changes:
The new implementation ensures that records with the same genomic position are properly randomized while maintaining correct positional ordering between different positions, fixing the reproducible bias in subsampling results.
Fixes #76