choose alt when possible, even if ref more frequent #3298
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Changelog Entry
To be copied to the draft changelog by merger:
vg deconstructno longer prints sites without altsDescription
Every now and then
vg deconstructcan print a site with only reference alleles (and AC=0), which doesn't make much sense. I think @ekg noticed this on his pggb output too.I checked and what's going on is related to the heuristic used to choose a single allele for a haplotype that (due to loops) runs through multiple alleles in the snarl: It chooses the most frequent allele and, in the case of a tie, takes the alt. So if a haplotype goes through an alt once and the ref twice, it will choose ref and it's possible that no sample takes the alt leading to one of these sites.
This PR changes it to always choose the alt in the event of a conflict, which I think is probably more intuitive as the alt is present in the haplotype.