ancestral polarization of individual genotypes

[wsdewitt]

Issue found by @ab08028:

When mutyper recodes REF/ALT/AC, it doesn’t seem to recode what 0 and 1 mean in the genotypes

Example: # original site:
NW_020656121.1  91648257    .   G   T   .   PASS    AA=T;AC=67;AN=68    GT  1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1
# I double checked that ancestral fasta was recoded to have AA=T

# site after mutyper variants:
NW_020656121.1  91648257    .   A   C   .   PASS    AA=T;AC=1;AN=68;mutation_type=AAT>ACT   GT  1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 0|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1 1|1

This affects downstream analysis of individual spectra, using mutyper spectra without the --population flag.

GT polarization code needed around here: https://github.com/harrispopgen/mutyper/blob/e9963c51cd304525ceed63e8c0b9bd8e4c8ba9a4/mutyper/cli.py#L112-L123