Fix bam2bcf indel calling: memset destroying consensus, uninit variable, wrong sizes#2531
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sirus20x6 wants to merge 3 commits intosamtools:developfrom
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Fix bam2bcf indel calling: memset destroying consensus, uninit variable, wrong sizes#2531sirus20x6 wants to merge 3 commits intosamtools:developfrom
sirus20x6 wants to merge 3 commits intosamtools:developfrom
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- bam2bcf_indel.c: Initialize K=0 at declaration to avoid using an uninitialized variable in the max-deletion loop (line ~783) which runs before K is reset at line ~791. - bam2bcf_iaux.c: Fix memset size in iaux_init_scores() to use n*sizeof(int) instead of n, since read_scores is int*. Without this, only 1/4 of the array (on most platforms) was being zeroed. - bam2bcf_iaux.c: Fix per-sample indel fraction denominator in iaux_init_types() to use ntot (per-sample read count) instead of naux (running cross-sample indel count), which produced incorrect filtering thresholds.
In bam2bcf_iaux.c, the memset after the first pass was zeroing `aux` (the nucleotide frequency counts) instead of `cns` (the consensus output buffer). This caused the consensus-building loop to see all-zero counts and produce 'N' for every position, discarding all insertion data. In bam2bcf.c, remove a duplicate memset(call->SCR, ...) that was a copy-paste error (two identical lines in a row).
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Summary
memset(aux, 0, ...)tomemset(cns, 0, ...)inbam2bcf_iaux.c— was zeroing nucleotide frequency counts just computed, causing the consensus builder to discard all insertion datamemset(read_scores, 0, n)tomemset(read_scores, 0, n * sizeof(int))— only zeroed 1/4 of the int arraynaux(cross-sample running total) tontot(per-sample count)Kinbam2bcf_indel.cmemset(call->SCR, ...)inbam2bcf.cTest plan
--indels-2.0produces correct insertion consensus sequences