debugging issue with HISAT2 QC

proost · Jul 25, 2017 · 82b7e81 · 82b7e81
1 parent 2d4b389
commit 82b7e81
Showing 1 changed file with 2 additions and 1 deletion.
diff --git a/pipeline/check/quality.py b/pipeline/check/quality.py
@@ -45,8 +45,9 @@ def check_hisat2(filename, cutoff=0, log=None):
 
     with open(filename, 'r') as f:
         lines = '\t'.join(f.readlines())
-        print(lines)
         for l in lines:
+            l = l.strip()
+            print(l)
             if "overall alignment" in l:
                 hits = re_mapped.search(l)
                 print(hits)