Uncompressed VCF variants

[fellen31]

Hi,

Thanks for writing this plugin!

I'm having trouble using variants/variantsMD5 on uncompressed VCFs, header seems to work fine.
Is it supported to be supported?

/Felix

[seppinho]

Correct, for some methods, we require a BGZF-compressed file (.vcf.gz) because we are using the query functionality of HTSJDK, which requires an index file. One approach could be to compress the VCF file using BGZIP and generate the index directly within the code. Would it also be possible for you to work directly with a .vcf.gz file?

[fellen31]

I see, in this case I wanted to snapshot the output of a software that only supports uncompressed VCF output.

If you already generate the index, then perhaps it would be okay to also compress the VCF within the code?

[seppinho]

I understand. I'll do my best to implement this feature. If you feel like contributing to a PR, let me know!