Fix vcfstats per-sample statistics using wrong FORMAT column index#2534
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sirus20x6 wants to merge 1 commit intosamtools:developfrom
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Fix vcfstats per-sample statistics using wrong FORMAT column index#2534sirus20x6 wants to merge 1 commit intosamtools:developfrom
sirus20x6 wants to merge 1 commit intosamtools:developfrom
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When --samples-file/-S is used and the sample order differs from the VCF, calc_sample_depth(), get_ad(), and get_iad() were called with the sample-list index (is) instead of the VCF column index (reader->samples[is]). This caused depth and allele depth values to be read from the wrong sample's FORMAT fields, producing incorrect per-sample statistics (PSC, PSI, VAF) while the sample names followed the file order. bcf_gt_type() was already correctly using reader->samples[is]. Now all FORMAT field accesses consistently use the VCF column index, while stats arrays remain indexed by the sample-list position. Fixes samtools#2469
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This is now added, with a test. Thank you |
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Summary
--samples-fileis used and sample order differs from the VCF, FORMAT field accessors (calc_sample_depth,get_ad,get_iad) used the subset indexisinstead of the VCF column indexreader->samples[is]ismpl = reader->samples[is]and used it consistently for all FORMAT data accessFixes #2469
Test plan
bcftools stats -s sample_listwith reordered sample list