Allow IUPAC codes on Match alleles

[Cristianetaniguti]

HapApp pipelines only replaces IUPAC codes present in the Ref and Alt alleles. IUPAC codes present in Match alleles should be ignored by the BIGr SNP calling algorithms.

• Decide if Ref and Alt with same IUPAC code should be kept or not. Example:

"AAGAAGTCAACCAGGC[R]CAAACCCAACCAAGCCTCCTTTTGGACTTCGAGGATTAAAGTACAGAACAAAATTTTGGCCTGGAACATTTTCAGCAGGTACTGATGCTCCT"
"AAGAAGTCAACCAGGC[R]CAAACCCAACCACGCCTCCTTTTGGACTTCGAGGATTAAAGTACAGAACAAAATTTTGGCCTGGAACATTTTCAGCAGGTACTGATGCTCCT"

• Change check MADC to distinguish Ref/Alt IUPAC from Match IUPAC
• Change madc2vcf_all to ignore IUPAC codes