Fix missing max(0,...) clamp on fasta.fetch() in add_normal_counts - #12
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Fix missing max(0,...) clamp on fasta.fetch() in add_normal_counts#12Bonney96 wants to merge 1 commit into
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…d_normal_counts - Move indel record list inside the per-interval loop so it resets each iteration; previously vcf_dicts accumulated across all intervals, causing duplicate/incorrect VCF output - Clamp fetch() start to max(0, ...) in add_normal_counts to prevent ValueError for variants near chromosome start - Rename vcf_results/vcf_dicts to all_indel_records/indel_vcf_records for clarity
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Summary
add_normal_counts()calledfasta.fetch(chrom, start_idx - flank, ...)at line 840 without clamping the start coordinate, causing aValueError: start out of rangewhen a variant sits withinflankbases of the chromosome start (e.g. IKZF2-KO-DNA hit this with start = -65).6e5b425) fixed the same pattern ingenerate_contig()but missed this call.max(0, start_idx - flank), consistent with all other fetch calls in the file.Reproduction
IKZF2-KO-DNA WGS sample hit a target site near chromosome start, crashing with: