Ensure that FixVariantCollisions works on chrY, chrX, chrM

[fabio-cunial]

Currently it works only if the GTs on such chromosomes have the usual format A/B. But this might not be the case.

[samuelklee]

ChrX is higher priority than chrY or chrM. Until recently, PanGenie was only run on 1-22 + X, so that's what we've been doing for KAGE+GLIMPSE. I believe the unreleased HGSVC3+HPRC PanGenie run does include Y, but it looks like they just hacked the calls in male samples to be homozygous on both X and Y: https://ftp.1000genomes.ebi.ac.uk/vol1/ftp/data_collections/HGSVC3/working/20240716_PanGenie-genotypes/20240716_PanGenie-genotypes_README.txt