This PR is to handle a bug with MNV handling (via auxiliary loci file) and the BAlleleFrequencyFormat.
Previously, this class used the SNP string directly from a BPMRecord (e.g. [A/G]) when canonicalizing the BAF for the VCF. But the auxiliary loci logic only overrides the plus_strand_alleles which are essentially a canonical representation of the SNP based on the raw SNP and the ref_strand.
The change to the class, is to use the plus_strand_alleles, which is the approach used in the GenotypeFormat class.
This PR is to handle a bug with MNV handling (via auxiliary loci file) and the
BAlleleFrequencyFormat.Previously, this class used the SNP string directly from a
BPMRecord(e.g. [A/G]) when canonicalizing the BAF for the VCF. But the auxiliary loci logic only overrides theplus_strand_alleleswhich are essentially a canonical representation of the SNP based on the raw SNP and theref_strand.The change to the class, is to use the
plus_strand_alleles, which is the approach used in theGenotypeFormatclass.