From: Diane Trout <diane@ghic.org>
Date: Wed, 2 Apr 2014 01:48:40 +0000 (-0700)
Subject: use autoopen to access fastq files
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=9ae32670d31d87b7e695b218b3fdbe4d94ac9a23

use autoopen to access fastq files
---

diff --git a/htsworkflow/pipelines/fastq.py b/htsworkflow/pipelines/fastq.py
index cf77005..47b2f83 100644
--- a/htsworkflow/pipelines/fastq.py
+++ b/htsworkflow/pipelines/fastq.py
@@ -40,5 +40,6 @@ def summarize_hiseq_fastq(stream):
 
 if __name__ == '__main__':
     import sys
-    with open(sys.argv[1], 'r') as instream:
+    from autoopen import autoopen
+    with autoopen(sys.argv[1], 'r') as instream:
         print summarize_hiseq_fastq(instream)