How does MAPGD determine major allele for multiple pooled samples, and can this be changed?

[peadams]

Hello,

I have 8 pooled samples in my mpileup, one of which is the ancestral population to the other 7 samples. I would like for my major alleles in the map.pol file to be called based on that sample, but it seems that MAPGD calls major alleles based on frequency across all 8 samples in the mpileup.

Is there a way to set one of my samples as the population to use for major/minor allele designation?

Thank you!

[rtraborn]

I just came across this issue (which was posted before I took the reins of the repo).
@matthew-ackerman has this been addressed? Let me know if it has and I'll close the issue.
Thanks,
Taylor