Include index of REF in Local Alleles (#5398)
Include index of REF in Local Alleles (#5398)

* Bind some variables

* Include index of REF in Local Alleles

Thus obtaining the allele for LGT[i] for all i is more straightforward:
    allele = alleles[LA[LGT[i]]]

Before we needed to do a LGT[i] == 0 check.

cseed/hail,hail-is/hail,cseed/hail,danking/hail,cseed/hail,hail-is/hail,danking/hail,cseed/hail,hail-is/hail,hail-is/hail,danking/hail,hail-is/hail,danking/hail,cseed/hail,hail-is/hail,cseed/hail,cseed/hail,danking/hail,danking/hail,danking/hail,cseed/hail,hail-is/hail,danking/hail,hail-is/hail