v1.4.0 - Claude update

Breaking Changes ⚠️

Default behavior for invalid alignments has changed:

• Previous versions: Invalid alignments (duplicates, failed QC, non-primary, supplementary) were kept by default, but was possible to skip them with --discard-invalid-alignments
• v1.4.0: Invalid alignments are now discarded by default for cleaner coverage analysis

New Features

• --keep-invalid-alignments: Restore legacy behavior to include invalid alignments in coverage calculation
• --discard-invalid-alignments: Still valid but does not change the behaviour
• Better handling of edge cases in alignment processing
• Expanded test suite (integration)
• CMake and Unit Tests

If your pipeline depends on the previous behaviour of including invalid alignments:

  # Old command (v1.3.x and earlier):
  covtobed input.bam > output.bed

  # New equivalent command (v1.4.0+):
  covtobed --keep-invalid-alignments input.bam > output.bed

For new workflows, the default behavior provides cleaner coverage tracks by excluding low-quality alignments.

Technical Details

Invalid alignments include:

• Duplicate reads (SAM flag 0x400)
• Failed quality control (SAM flag 0x200)
• Non-primary alignments (SAM flag 0x100)
• Supplementary alignments (SAM flag 0x800)