bug fix: some cigar codes caused find_intersecting_snps to crash beca…

…use of typo in snptable
bmvdgeijn · Sep 13, 2016 · 475f923 · 475f923
1 parent 6274f09
commit 475f923
Showing 1 changed file with 2 additions and 2 deletions.
diff --git a/mapping/snptable.py b/mapping/snptable.py
@@ -392,11 +392,11 @@ def get_overlapping_snps(self, read):
                 # in these cases, presumably reference version of read
                 # would map to same location (with higher score).
 
-            elif seq_type == BAM_CHARD_CLIP:
+            elif op == BAM_CHARD_CLIP:
                 # these bases not included in read or genome
                 pass
 
-            elif seq_type == BAM_CPAD:
+            elif op == BAM_CPAD:
                 # like an insert, likely only used in multiple-sequence
                 # alignment where inserts may be of different lengths
                 # in different seqs