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Adds readme = "README.md" to pyproject.toml so the long description renders on the PyPI project page. Updates ChangeLog for v4.4.1. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
For read_2 (reverse), the reference_segment is constructed starting `padding` bases before self.position to allow room for deletions after reverse_complement. apply_mutations was computing the intra-segment index using self.position, which caused mutations to be placed padding (= read_len // 5) bases too early in the segment. After reverse_complement this manifested as indels appearing at a different reference coordinate in read_2 than in read_1. Fix: add segment_start attribute to Read, set to the actual reference coordinate of reference_segment[0]. apply_mutations now subtracts segment_start instead of position when computing the index. Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Fix indel position offset in paired-end reverse reads
…sition Add regression tests for PR 276 indel position in reverse reads
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