bcftools annotate produces truncated vcf with exit code 0

[dennishendriksen]

bcftools annotate can exit with exit code 0 when processing an invalid vcf with the ASCII NULL value for a genotype value for a FORMAT field. This can result in a truncated vcf being produced (after the third error was encountered?).

bcftools view exits with a non-zero exit code as expected.

$ zgrep -vc "^#" bcftools_exitcode.vcf.gz
5

$ bcftools annotate bcftools_exitcode.vcf.gz --output-type v --output bcftools_exitcode_annotated.vcf
[E::vcf_parse_format_fill5] Couldn't read GT data: value not a number or '.' at chr11:72608665
[E::vcf_parse_format_fill5] Couldn't read GT data: value not a number or '.' at chr11:114064239
$ echo $?
0
$ grep -vc "^#" bcftools_exitcode_annotated.vcf
1

$ bcftools view bcftools_exitcode.vcf.gz > /dev/null
[E::vcf_parse_format_fill5] Couldn't read GT data: value not a number or '.' at chr11:72608665
[E::vcf_parse_format_fill5] Couldn't read GT data: value not a number or '.' at chr11:114064239
Error: VCF parse error
$ echo $?
8

bcftools_exitcode.vcf.gz

[pd3]

This is now fixed, thank you for reporting the problem