Fix vcfannotate type mismatch, null deref, and stale buffer#2524
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sirus20x6 wants to merge 1 commit intosamtools:developfrom
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Fix vcfannotate type mismatch, null deref, and stale buffer#2524sirus20x6 wants to merge 1 commit intosamtools:developfrom
sirus20x6 wants to merge 1 commit intosamtools:developfrom
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1. setter_ARinfo_int32 (line 788): Used bcf_get_info_float to read int32 data into an int32 buffer. Changed to bcf_get_info_int32. 2. setter_info_int and setter_info_real: When flushing merged values for Number=A/R tags, `tab` (the annotation line) is NULL, causing a null pointer dereference. Fall back to line->n_allele and line->d.allele when tab is NULL. 3. vcf_setter_format_real: determine_ploidy was called with args->tmpi and args->tmpi2 (int buffers) instead of the float buffers (args->tmpf and args->tmpf2) that actually hold the format data. Cast the float buffers to int* since htslib sentinel values (missing/vector_end) share the same bit patterns between float and int32 representations.
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pd3
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This is not a good fix, it introduces a bug, casting forcibly |
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Summary
bcf_get_info_floattobcf_get_info_int32insetter_ARinfo_int32— was reading integer data through the float API, corrupting valuestabinsetter_info_intandsetter_info_realmerge-flush paths — usesline->n_allele/line->d.allelewhentabis NULL for Number=A/R tagsdetermine_ploidyinvcf_setter_format_realto use float buffers instead of stale int buffersTest plan