bcftools annotate --mark-sites ignores --min-overlap

[lindenb]

Hi,

unless I'm wrong --mark-sites in bcftools annotate ignores the parameters --min-overlap.
The Flag is always added event if the overlap isn't large enough.

In my test there are 3572 variants with or without --min-overlap "0.8:0.8"

./bcftools annotate  --mark-sites +IN_DGV --min-overlap "0.8:0.8" -a dgv.bed.gz -h dgv.header.txt -c 'CHROM,POS,END,DGV'  in.bcf  |\
  ./bcftools view -G --no-header | grep IN_DGV -c
3572

./bcftools annotate  --mark-sites +IN_DGV -a dgv.bed.gz -h dgv.header.txt -c 'CHROM,POS,END,DGV'  in.bcf |\
  ./bcftools view -G --no-header | grep IN_DGV -c
3572

but there are only 545 variants overlaping the annotations.

./bcftools annotate  --mark-sites +IN_DGV --min-overlap "0.8:0.8" -a dgv.bed.gz -h dgv.header.txt -c 'CHROM,POS,END,DGV' in.bcf |\
  ./bcftools view -G --no-header | grep -c 'DGV='
545

same command without min-overlap

./bcftools annotate  --mark-sites +IN_DGV  -a dgv.bed.gz -h dgv.header.txt -c 'CHROM,POS,END,DGV' in.bcf |\
  ./bcftools view -G --no-header | grep -c 'DGV='
3572

[pd3]

Thank you for the bug report, this is now fixed.