bcftools consensus: Directory of chain file does not exist => segmentation fault

[karel-brinda]

When I call bcftools consensus with the -c parameter (to create a chain file), non-existence of the chain file's directory causes Segmentation fault: 11.

Examples:

1. Non-existing directory:

On-y-go:test karel$ "/Users/karel/.smbl/bin/bcftools" consensus -c "a/a.chain" -f "test_experiment/1_reference/00000.fa" "test_experiment/7_vcf/00000.vcf.gz" > "test_experiment/1_reference/00001.fa"
[W::vcf_parse] INFO 'mt' is not defined in the header, assuming Type=String
Segmentation fault: 11
On-y-go:test karel$ echo $?
139

2. Existing directory:

On-y-go:test karel$ "/Users/karel/.smbl/bin/bcftools" consensus -c "a.chain" -f "test_experiment/1_reference/00000.fa" "test_experiment/7_vcf/00000.vcf.gz" > "test_experiment/1_reference/00001.fa"
[W::vcf_parse] INFO 'mt' is not defined in the header, assuming Type=String
On-y-go:test karel$ echo $?
0

Version of bcftools

On-y-go:test karel$ ~/.smbl/bin/bcftools 

Program: bcftools (Tools for variant calling and manipulating VCFs and BCFs)
Version: b3257c1 (using htslib 4c82a74)
...

[jmarshall]

Thanks for the report. It's a standard-issue failure to check the fopen() return value…