Enable FilterVcf to filter "sites only" VCFs

[yfarjoun]

Description

Currently, FilterVcf will filter entirely a sites-only vcf since "all" the genotypes are filtered (as there are no genotypes) and when a sites has all the genotypes filtered it filters out the site...This modification changes behavior so that a sites only VCF will not be filtered due to "all" its (non-existent) genotypes.

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[coveralls]

Coverage remained the same at 77.055% when pulling c8875e2 on yf_fix_vcf_filter_for_sites_only_vcf into 3904528 on master.

[gbggrant]

👍

[nh13]

@yfarjoun I'd suggest @tfenne take a look since he wrote that line, and also since it isn't backwards compatible!

[yfarjoun]

ok. I'll wait to hear from him! thanks for the heads-up!

[tfenne]

Thanks for the heads up @nh13. I think the change is fine. My goal was to enable filtering of sites where the site-level filters pass, but all the genotypes got filtered out. I think this still does the same thing so long as there are samples with non-hom-ref genotype present in the file.