`bcftools view` does not return an error code when invalid character in FORMAT field

[jkmatila]

When there is an invalid character in a FORMAT field, bcftools will print an error message but will exit with status code 0, indicating success.

I would expect there be to an error code returned, since encountering this error will result in partial output.

A small VCF file for reproducing the problem can be found in repro.zip

Steps to reproduce:

$ bcftools --version
bcftools 1.4
Using htslib 1.4
Copyright (C) 2016 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.

$ bcftools view repro.vcf
[E::vcf_parse_format] Invalid character '.' in 'SB' FORMAT field at 1:115256530
##fileformat=VCFv4.1
##FILTER=<ID=PASS,Description="All filters passed">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=SB,Number=4,Type=Integer,Description="Per-sample component statistics which comprise the Fisher's Exact Test to detect strand bias.">
##contig=<ID=1,length=249250621,assembly=b37>
##bcftools_viewVersion=1.4+htslib-1.4
##bcftools_viewCommand=view repro.vcf; Date=Wed Apr  5 19:10:19 2017
#CHROM	POS	ID	REF	ALT	QUAL	FILTER	INFO	FORMAT	sample

$ echo $?
0

Observed: zero exit code. Expected: a non-zero exit code.

[pd3]

Thank you for the bug report. It is fixed now by e984014