debugging issue with HISAT2 QC

proost · Jul 25, 2017 · 2d4b389 · 2d4b389
1 parent 2940d4c
commit 2d4b389
Showing 1 changed file with 1 addition and 0 deletions.
diff --git a/pipeline/check/quality.py b/pipeline/check/quality.py
@@ -45,6 +45,7 @@ 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:
             if "overall alignment" in l:
                 hits = re_mapped.search(l)