diff --git a/slamdunk/utils/SNPtools.py b/slamdunk/utils/SNPtools.py index 10d59c2..0ba4778 100644 --- a/slamdunk/utils/SNPtools.py +++ b/slamdunk/utils/SNPtools.py @@ -28,12 +28,13 @@ def __init__(self, vcfFile): self._agSNPs = {} def _addSNP(self, snp): + if(snp[3].upper() == "T" and snp[4].upper() == "C"): key = snp[0] + snp[1] self._tcSNPs[key] = True if(snp[3].upper() == "A" and snp[4].upper() == "G"): - key = snp[0] + str(int(snp[1]) - 1) + key = snp[0] + snp[1] self._agSNPs[key] = True def read(self):