2.3.0

Bug Fixes

• Correct typo in htslib configuration path (7176a53)
• Add sam_hdr_destroy declaration to prevent double-free (81dd65d)
• Add error checking and safe pointer initialization in BwaIndex (67399f0)
• Add type annotations and update stub files for mypy compliance (6263aa0)
• Pre-compile bwa into static library to eliminate parallel build race condition (3d4a5b8)

Documentation

• Revamp README with quick start examples (dda1484)
• Improve docstrings across public API (30a4bb2)
• Reorganize api.rst with task-oriented examples (7af210c)
• Add comment explaining QEMU usage in wheel builds (7c84d45)
• Add thread-safety warning to set_bwa_verbosity (2136eb7)

Features

• Drop Python 3.9 support, add Python 3.13 and 3.14 (#120) (42b60dc)
• Comprehensive code quality and performance improvements (2e7b496)
• Improve type hints for better IDE support (886ff63)

Performance

• Add caching for htslib build artifacts (895e6e4)

Refactor

• Consolidate error checking with shared utility functions (7e9cf6d)

Styling

• Fix import formatting in stub files (5ac9d25)
• Fix formatting in test_resource_management.py (c730f21)

Testing

• Add comprehensive error handling and resource management tests (1c00c4b)

2.2.0

Features

• Add an optimized method for XA parsing (#112) (bfa8fbe)
• Add the 'ea' tag to bwa aln in case the search exits early (#111) (cf49ea7)

2.1.0

Documentation

• Fix links to logo (#103) (e3e9fc1)

Features

• Remove types arguments (#105) (489887d)
• Add the bwa aln -m option (#107) (b0fad41)

2.0.1

Bug Fixes

• Fix the body for the git-cliff changelog (#99) (e0f06a9)

Features

• Libdeflate, lzma, curl, and bz2 are now optional (#101) (5da0c3f)

Miscellaneous Tasks

• Update git-cliff CI action to v4 (#97) (0b220ce)

2.0.0

[2.0.0] - 2025-04-01

This is a major version release, as #91 changed the type signatures for the BwaAlnOptions and BwaMemOptions constructors.

Chore

• (release) Bump to 2.0.0 (#96)

Feat

• Add option defaults in constructor (#91)
• Updating style, formatting, and linting (#93)

Fix

• Always configure in htslib (#92)
• Always run cython test code, previously skipped (#95)

1.6.0

[1.6.0] - 2025-04-01

Chore

• (release) Bump to 1.6.0 (#87)

Feat

• Further improve bwa mem speed (#86)

1.5.2

[1.5.2] - 2025-03-28

Chore

• (release) Bump to 1.5.2

Fix

• Add missing htslib source files (#85)

1.5.1

[1.5.1] - 2025-03-27

Chore

• Fix link to conventional commits (#82)
• Update classifiers in build (#83)
• (release) Bump to 1.5.1

Feat

• Use htslib directly to create BAM records (#84)

1.5.0

[1.5.0] - 2025-03-18

Chore

• Update CIBW_MANYLINUX_X86_64_IMAGE in wheels build to manylinux_2_28 (#63)
• Add fast fail for tests and parallelize extension builds (#65)
• Add const to various C imports (#66)
• Update poetry to 2.1.1 (#69)
• Add pybwa version to the wheel name and suffix .whl (#70)
• Add test coverage for bwa aln returning XN (#71)
• Fix website link in readme
• Update tests on push (#81)
• (release) Bump to 1.5.0

Ci

• Use ubuntu-22.04-arm for manylinux_aarch64 and musllinux_aarch64 (#67)
• Add retry to building extensions and building wheels. (#73)
• Fix extension building fallback (#76)

Feat

• Allow switching BWA verbosity (#80)

Fix

• Plug a few memory leaks (#74)

1.4.8

[1.4.8] - 2025-03-14

Chore

• Add doi to README (#61)
• (release) Bump to 1.4.8