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Fix vcfcnv OOB read with control sample and AA skip mismatch #2529

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Fix vcfcnv OOB read with control sample and AA skip mismatch #2529

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10 changes: 6 additions & 4 deletions vcfcnv.c
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Original file line number Diff line number Diff line change
Expand Up @@ -871,8 +871,9 @@ static int update_sample_args(args_t *args, sample_t *smpl, int ismpl)
for (i=0; i<args->nsites; i++)
{
float baf = smpl->baf[i];
if ( baf>4/5.) continue; // skip AA genotypes
if ( baf>0.5 ) baf = 1 - baf; // the bands should be symmetric
if ( baf<1/5.) continue; // skip RR,AA genotypes
if ( baf<1/5.) continue; // skip RR genotypes

double prob_cn3 = args->tmpf[k++];
baf_dev2 += prob_cn3 * (baf - mean_cn3)*(baf - mean_cn3);
Expand Down Expand Up @@ -1037,7 +1038,7 @@ static void cnv_flush_viterbi(args_t *args)
for (isite=0; isite<args->nsites; isite++)
{
int state = vpath[args->nstates*isite];
double *pval = fwd + isite*args->nstates;
double *pval = fwd + (isite+1)*args->nstates;

qual += pval[start_cn];

Expand Down Expand Up @@ -1157,10 +1158,11 @@ static void cnv_next_line(args_t *args, bcf1_t *line)
if ( !(baf_fmt = bcf_get_fmt(args->hdr, line, "BAF")) ) return;
if ( args->lrr_bias>0 && !(lrr_fmt = bcf_get_fmt(args->hdr, line, "LRR")) ) return;

float baf1,lrr1,baf2,lrr2;
float baf1,lrr1,baf2=-1,lrr2=0;
int ret = 0;
ret += parse_lrr_baf(&args->query_sample, baf_fmt,lrr_fmt,&baf1,&lrr1);
ret += parse_lrr_baf(&args->control_sample,baf_fmt,lrr_fmt,&baf2,&lrr2);
if ( args->control_sample.name && args->control_sample.idx >= 0 )
ret += parse_lrr_baf(&args->control_sample,baf_fmt,lrr_fmt,&baf2,&lrr2);
if ( !ret ) return;

// Realloc buffers needed to store observed data and used by viterbi and fwd-bwd
Expand Down