When reading a VCF file, in the case that all ingroup and outgroup alleles are missing, the program would crash because it would still try to select an outgroup allele as a fixed difference. This PR resolves that issue and also adds a check for invariant sites to be skipped in case the input file is a gvcf.
When reading a VCF file, in the case that all ingroup and outgroup alleles are missing, the program would crash because it would still try to select an outgroup allele as a fixed difference. This PR resolves that issue and also adds a check for invariant sites to be skipped in case the input file is a gvcf.