statSTR handling of chrY

[hopedisastro]

I get the following error when running statSTR on a VCF with chrY loci genotyped by ExpansionHunter:

File "/root/micromamba/lib/python3.10/site-packages/trtools/utils/utils.py", line 312, in GetHardyWeinbergBinomialTest if gt[1] not in allele_freqs.keys(): IndexError: tuple index out of range

I think this is because the 'GT' is not in the format of two numbers eg '0/1' or '1/1' but just one integer eg '0' or '1' to represent the hemizygous chrY.

[br2890]

Just wanted to check on the above. Would the tools now support chrY positions?

Just noticed the following in the description, but would be great if does now support haploid calls:

TRTools only currently supports diploid genotypes. Haploid calls, such as those on male chrX or chrY, are not yet supported but should be coming soon.