gtcheck -i qry|gt prefix not removed

[aheinzel]

Dear all,

bcftools 1.22 gtcheck site filter -i expressions referring to either query or genotype fields using the qry or gt prefix do currently not work.

Steps to reproduce

#!/bin/bash

dummy_vcf_file=$(cat <<'EOF'
##fileformat=VCFv4.1
##INFO=<ID=DP,Number=1,Type=Integer,Description="Total Depth">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	s1
chr1	1	.	A	T	.	.	DP=10	GT	1/1
EOF
)

for fout in g.vcf.gz q.vcf.gz
do
   echo "${dummy_vcf_file}" | bgzip > "${fout}"
   tabix -p vcf "${fout}"
done


echo "##VERSION INFO"
bcftools --version


printf "\n\n##no site filter expression\n"
bcftools gtcheck -g g.vcf.gz q.vcf.gz | tail -1


printf "\n\n##site filter without prefix (filters both gt and qry)\n"
bcftools gtcheck -i "INFO/DP>10" -g g.vcf.gz q.vcf.gz | tail -1

printf "\n\n##site filter with qry prefix\n"
bcftools gtcheck -i "qry:INFO/DP>10" -g g.vcf.gz q.vcf.gz | tail -1

Output

##VERSION INFO
bcftools 1.22
Using htslib 1.22
Copyright (C) 2025 Genome Research Ltd.
License Expat: The MIT/Expat license
This is free software: you are free to change and redistribute it.
There is NO WARRANTY, to the extent permitted by law.


##no site filter expression
INFO:   Time required to process one record .. 0.000009 seconds
DCv2    s1      s1      0.000000e+00    0.000000e+00    1       1


##site filter without prefix (filters both gt and qry)
DCv2    s1      s1      0.000000e+00    0.000000e+00    0       0


##site filter with qry prefix
[filter.c:3463 filters_init1] Error: the tag "qry:INFO" is not defined in the VCF header

Expected behaviour

bcftools gtcheck -i "qry:INFO/DP>10" -g g.vcf.gz q.vcf.gz should run and restrict the comparison to sites with depth > 10 in the query data set.

Actual behaviour

Command errors out

[filter.c:3463 filters_init1] Error: the tag "qry:INFO" is not defined in the VCF header

Additional information

Looking at the source code it appears that the qry: prefix is not "stripped" from the filter expression before assignment to args->qry_filter_str and thus the prefix is later on included when passing the expression to filter_init.

bcftools/vcfgtcheck.c

Line 1318 in 0949c4d

args->qry_filter_str = optarg;

In similar cases like e.g. sample filter

bcftools/vcfgtcheck.c

Line 1394 in 0949c4d

else if ( !strncasecmp("qry:",optarg,4) ) args->qry_samples = optarg+4;

the pointer is incremented before assignment to remove the prefix

[pd3]

Thank you for the bug report, this is now fixed