Bugfix: Reverse strand A->G SNP coordinates.

t-neumann · Feb 8, 2019 · 704df5e · 704df5e
1 parent 355169f
commit 704df5e
Showing 1 changed file with 2 additions and 1 deletion.
diff --git 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):