bcftools gtcheck --no-HWE-prob segfaults trying to access uninitialized args->nmatch array

[freeseek]

If you run bcftools gtcheck --no-HWE-prob the array args->nmatch is not initialized:

if ( args->calc_hwe_prob )
{
    // prob of the observed sequence of matches given site AFs and HWE
    args->hwe_prob = (double*) calloc(args->npairs,sizeof(*args->hwe_prob));
    if ( !args->hwe_prob ) error("Error: failed to allocate %.1f Mb. Run with --no-HWE-prob to save some memory.\n", args->npairs*sizeof(*args->hwe_prob)/1e6);
    args->nmatch = (uint32_t*) calloc(args->npairs,sizeof(*args->ncnt));         // number of matches, used only with calc_hwe_prob
    if ( !args->nmatch ) error("Error: failed to allocate %.1f Mb.\n", args->npairs*sizeof(*args->ncnt)/1e6);
}

At the end of the run gtcheck writes the report with the following command:

if ( args->ndiff )
{
    ksprintf(&args->kstr,"DCv2\t%s\t%s\t%u\t%e\t%u\t%u\n",
            args->qry_hdr->samples[iqry],
            args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
            args->ndiff[idx],
            (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0,
            args->ncnt[idx],
            args->nmatch[idx]);
}
else
{
    ksprintf(&args->kstr,"DCv2\t%s\t%s\t%e\t%e\t%u\t%u\n",
            args->qry_hdr->samples[iqry],
            args->gt_hdr?args->gt_hdr->samples[igt]:args->qry_hdr->samples[igt],
            args->pdiff[idx],
            (args->calc_hwe_prob && args->nmatch[idx]) ? args->hwe_prob[idx]/args->nmatch[idx] : 0,
            args->ncnt[idx],
            args->nmatch[idx]);
}

But there is no check for args->calc_hwe_prob when accessing args->nmatch[idx]. The two instances of args->nmatch[idx] should be replaced with args->calc_hwe_prob ? args->nmatch[idx] : 0 or something similar

[pd3]

The bug was introduced by 983e610ab. It is now fixed, thank you for reporting it.