Fix missing header finalization and unchecked faidx return#2536
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sirus20x6 wants to merge 1 commit intosamtools:developfrom
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Fix missing header finalization and unchecked faidx return#2536sirus20x6 wants to merge 1 commit intosamtools:developfrom
sirus20x6 wants to merge 1 commit intosamtools:developfrom
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In gensample_to_vcf (vcfconvert.c), add the missing bcf_hdr_add_sample(header, NULL) finalization call after the sample addition loop, matching the pattern used in haplegendsample_to_vcf and other converters. In indel_ctx_type (vcfstats.c), check faidx_fetch_seq return for NULL before dereferencing. If the chromosome is absent from the reference, return the default indel length with nrep=0, nlen=0 instead of crashing with a NULL pointer dereference.
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pd3
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Mar 31, 2026
| *se = 0; | ||
| bcf_hdr_add_sample(args->header,samples[i]); | ||
| } | ||
| bcf_hdr_add_sample(args->header,NULL); |
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This is no longer required, see comments in vcf.c
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Resolved via 8cd70c9, the change in vcfconvert.c is not required. |
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Summary
bcf_hdr_add_sample(args->header, NULL)ingensample_to_vcf(vcfconvert.c) — header was not finalized after adding samples, matching the pattern inhaplegendsample_to_vcffaidx_fetch_seqreturn inindel_ctx_type(vcfstats.c) — prevents NULL dereference when chromosome is not in the referenceTest plan
bcftools convert --gensample2vcfwith sample filesbcftools stats --ref-filewith mismatched reference