Skip to content

Fix vcfstats per-sample statistics using wrong FORMAT column index #2534

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Closed
sirus20x6 wants to merge 1 commit into from
+7 −5
Closed

Fix vcfstats per-sample statistics using wrong FORMAT column index #2534

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
12 changes: 7 additions & 5 deletions vcfstats.c
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -1103,8 +1103,10 @@ static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int
int is;
for (is=0; is<args->files->n_smpl; is++)
{
int ismpl = reader->samples[is]; // VCF column index for this sample

// Determine depth
int dp = calc_sample_depth(args,is,ad_fmt_ptr,dp_fmt_ptr);
int dp = calc_sample_depth(args,ismpl,ad_fmt_ptr,dp_fmt_ptr);
if ( dp>0 )
{
(*idist(&stats->dp, dp))++;
Expand All @@ -1116,7 +1118,7 @@ static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int
int ial, jal, gt=GT_UNKN;
if ( gt_fmt_ptr )
{
gt = bcf_gt_type(gt_fmt_ptr, reader->samples[is], &ial, &jal);
gt = bcf_gt_type(gt_fmt_ptr, ismpl, &ial, &jal);
sample_gt_stats(args,stats,line,is,gt,ial,jal);
}

Expand All @@ -1126,12 +1128,12 @@ static void do_sample_stats(args_t *args, stats_t *stats, bcf_sr_t *reader, int
float iad = 0, jad = 0;
if ( gt==GT_UNKN ) // GT not available
{
iad = get_ad(line,ad_fmt_ptr,is,&ial);
iad = get_ad(line,ad_fmt_ptr,ismpl,&ial);
}
else if ( gt!=GT_UNKN )
{
iad = ial==0 ? 0 : get_iad(line,ad_fmt_ptr,is,ial);
jad = jal==0 ? 0 : get_iad(line,ad_fmt_ptr,is,jal);
iad = ial==0 ? 0 : get_iad(line,ad_fmt_ptr,ismpl,ial);
jad = jal==0 ? 0 : get_iad(line,ad_fmt_ptr,ismpl,jal);
}
if ( iad )
{
Expand Down