1.0.0

Main improvements

• Significantly improved consensus calling accuracy around small deletions
• Significantly improved consensus calling accuracy around large clip-dominant deletions in --realign mode for some alignments
• Fixed issue with difflib.SequenceMatcher where identifying overlaps in clip-dominant regions could fail unexpectedly
  • Fixes related TypeError with --realign enabled (reported by @sivico26)
• Faster installation and consensus generation

Other changes

• Added support for Python versions up to 3.13, offering significant performance improvements
• Minimum Python version increased from 3.6 to 3.8
• Replaced Biopython with dnaio for sequence IO
• Testing improvements:
  • Expected consensus sequences now are validated by the test suite, guarding against regressions
  • Added clip-dominant test case helpfully shared by @sivico26 (#23)
  • Test suite now runs in CI with both newest and oldest supported Python versions
• Moved to pyproject.toml with Flit build backend
• Added Ruff pre-commit

Breaking changes

• Removed:
  • kindel variants
  • Plotting functions other than kindel plot-clips (renamed in this release to kindel plot)

Please open an issue if this release causes problems or breaks your workflow.

0.4.4

• Python 3.8
• min_depth defaults to 1 in both CLI and Python API (CLI default was 2)
• Removes <unknown description> from generated fasta headers

0.4.3

• Fixes crash for reference sequences <100bp
• Counts SAM 1.4 CIGAR X records
• Changes to stdout report format

0.4.2

• Works with Minimap2 BAMs
• Tested against bacterial alignment (performance is poor; be warned)

0.4.1

Fixes SAM parsing regression in 0.4.0 (thanks to @mdshw5)

0.4.0

• Support for BAMs with more than one reference chromosome
  • Generates a consensus sequence for each reference contig with one or more primary alignments

0.2.0

• Refactored handling of consensus inference at clip-dominant regions
• Basic tests and CI

0.3.0

• Basic documentation and JOSS paper
• Tidies up tabular output of weights()

0.1.4

Reconciles substitutions and CIGAR specified indels