From 2d4b389ba735323b2bdc307226de392bc8e52ee9 Mon Sep 17 00:00:00 2001
From: sepro <sebastian.proost@gmail.com>
Date: Tue, 25 Jul 2017 10:38:43 +0200
Subject: [PATCH] debugging issue with HISAT2 QC

---
 pipeline/check/quality.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/pipeline/check/quality.py b/pipeline/check/quality.py
index 8bd7640..2cc70e0 100644
--- 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)