fix: count WES samples in AN — capture index missed non-chr and chrMT BEDs - #35

Merged

dlopez-bioinfo merged 12 commits into

fix/capture-index-chrom-normalization

Jul 20, 2026

Commits on Jul 20, 2026

fix(capture): normalize BED chrom names in CaptureIndex
dlopez-bioinfo
committed
bc7727a
feat(capture): warn when a capture BED matches no known chromosome
dlopez-bioinfo
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828ba39
test(capture): cover BEDs without the 'chr' prefix
dlopez-bioinfo
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89e277f
docs: explain why variant-info carrier counts exceed query counts
dlopez-bioinfo
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506bce0
fix(constants): map chrMT and lowercase chrom names to canonical form
dlopez-bioinfo
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a7d8fb5
refactor(capture): expose chrom introspection instead of private _index
dlopez-bioinfo
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9443052
fix(capture): report unusable capture BEDs instead of crashing on them
dlopez-bioinfo
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d2ea250
refactor(capture): keep the PyRanges object out of capture pickles
dlopez-bioinfo
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44bbfa1
fix(build): report contigs dropped during chrom discovery
dlopez-bioinfo
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ca865d9
perf(query): precompute targeted capture indices outside the position loop
dlopez-bioinfo
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ca7f3ab
docs: document chrom normalization and capture diagnostics
dlopez-bioinfo
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b1503ee
chore: drop uv.lock
dlopez-bioinfo
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202db15