io.py

bqual = read.alignment.query_qualities[qpos] added
uci-cbcl · Jun 30, 2016 · 634ff3d · 634ff3d
1 parent ae1585e
commit 634ff3d
Showing 1 changed file with 6 additions and 6 deletions.
diff --git a/pyloh/preprocess/io.py b/pyloh/preprocess/io.py
@@ -88,20 +88,20 @@ def _parse_pileup_column(self, pileup_column):
             if read.is_del:
                 continue
 
-            if hasattr(read, 'qpos') == True:
-                qpos = read.qpos
-            elif hasattr(read, 'query_position') == True:
+            if hasattr(read, 'query_position') == True:
                 qpos = read.query_position
+                bqual = read.alignment.query_qualities[qpos]
+            elif hasattr(read, 'qpos') == True:
+                qpos = read.qpos
+                bqual = ord(read.alignment.qual[qpos]) - ascii_offset 
             else:
                 raise Exception("Error in pysam qpos/query_position.")
 
             mqual = read.alignment.mapq
 
             if mqual < self.min_mqual:
                 continue            
-
-            bqual = ord(read.alignment.qual[qpos]) - ascii_offset            
-
+
             if bqual < self.min_bqual:
                 continue