Reference allele not set in vcf (reference fasta hardcoded)

[kpalin]

Hi,

setting of the reference allele in the vcf fails (informatively, thank you for that) in almost all environments.

The issue is at https://github.com/DecodeGenetics/popSTR/blob/3a5ca742116bee78490e8bbb6e2c47ffc7781334/msGenotyper.cpp#L549

A simple fix would be to use samtools faidx $REF_PATH region. The environment variable REF_PATH is (should be) standard.