Due to the stringency of EBI's vcf-validator and feedback from users who mostly use the --no_vcf_validate option, we can probably remove it completely. Some tests I ran with fake VCF files were actually caught by cyvcf2, so I think we don't even need a bcftools query -l-type check (it doesn't even reach the validation part since cyvcf2 catches it earlier).
I suggest we leave it to the user to make sure their VCFs are 'valid'.
Due to the stringency of EBI's
vcf-validatorand feedback from users who mostly use the--no_vcf_validateoption, we can probably remove it completely. Some tests I ran with fake VCF files were actually caught bycyvcf2, so I think we don't even need abcftools query -l-type check (it doesn't even reach the validation part since cyvcf2 catches it earlier).I suggest we leave it to the user to make sure their VCFs are 'valid'.
Resolves #124