Clarify call_genotype_phased for ploidy=1

[hyanwong]

I assume that if this is haploid data, we don't need a call_genotype_phased array to show that the data is phased? Unless the suggestion is that haploid data without a call_genotype_phased array could be pseudohaploid?

[jeromekelleher]

call_genotype_phased is optional I believe, so it's up to implementations whether they include it or not. If it's not present, then genotypes are assumed unphased. One could debate whether haploids are phased or unphased, but I think the interpretation is clear either way.

[hyanwong]

I think that's what I mean. If I have phased haploids, am I required to provide a call_genotype_phased array, or is this implicit. It's not clear to me?

[jeromekelleher]

I don't think phased/unphased has any meaning for haploids, so there's no real point in trying to specify what it does or doesn't mean here.