bcftools annotate -x INFO does not remove INFO/END when output set in binary mode

[freeseek]

Generate the following VCF file:

(echo "##fileformat=VCFv4.1"
echo "##contig=<ID=1,assembly=b37,length=249250621>"
echo "##ALT=<ID=CN2,Description=\"Copy number allele: 2 copies\">"
echo "##INFO=<ID=END,Number=1,Type=Integer,Description=\"End coordinate of this variant\">"
echo -e "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"
echo -e "1\t668630\t.\tG\t<CN2>\t.\t.\tEND=850204") > in.vcf

Then the following commands output the variant:

$ bcftools annotate --no-version -x INFO -Ob -o in.bcf in.vcf
$ bcftools index -f in.bcf
$ bcftools view --no-version -H -r 1:850204-850204 in.bcf
1	668630	.	G	<CN2>	.	.	.

While the following commands output nothing:

$ bcftools annotate --no-version -x INFO -Oz -o in.vcf.gz in.vcf
$ bcftools index -f in.vcf.gz
$ bcftools view --no-version -H -r 1:850204-850204 in.vcf.gz

Similarly, when using INFO/END rather than INFO the output is empty again:

$ bcftools annotate --no-version -x INFO/END -Ob -o in.bcf in.vcf
$ bcftools index -f in.bcf
$ bcftools view --no-version -H -r 1:850204-850204 in.bcf

My guess is that, when bcftools annotate -x INFO is used, the command forgets to set the line->rlen field to the length of the reference allele.

[pd3]

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