fix: skip overlapping variants in get_diffs_sparse (#153)#154
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Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
Co-Authored-By: Claude Sonnet 4.6 <noreply@anthropic.com>
…ction logic Spanning deletion markers (*) in phased VCFs were incorrectly counted as negative ilen contributions in get_diffs_sparse, undersizing the output buffer and truncating ragged haplotypes at the 3' end. Fixes #153
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Summary
get_diffs_sparse()was summingilenfor all variants without skipping overlaps, causing*(spanning deletion) alleles to double-count their parent deletion's length changeref_idxtracking (3 lines) to match the overlap-skipping logic already inreconstruct_haplotype_from_sparse()Root cause
When a phased VCF contains a
*allele (e.g.GCGCCA→*, ilen = −5),get_diffs_sparsecounted it as an independent deletion. But*marks a position already consumed by an upstream deletion on the same haplotype — the reconstruction correctly skipped it, but the buffer-sizing step did not. Result: output buffer too small → 3′ truncation.Test plan
pixi run -e dev pytest tests/dataset/test_issue_153.py -v— regression test (hap1=42641, hap2=42647)pixi run -e dev test— full suite (365 pass, 5 skip, 2 xfail)Closes #153
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