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

popSTR/msGenotyper.cpp

Line 549 in 3a5ca74

cmdStream << "/odinn/users/snaedisk/bin/crop_fasta /odinn/data/reference/Homo_sapiens-deCODE-hg38/Sequence/WholeGenomeFasta/genome.fa " << marker.chrom << ":" << toCString(str) << "-" << marker.end;

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