use autoopen to access fastq files

diff --git a/htsworkflow/pipelines/fastq.py b/htsworkflow/pipelines/fastq.py
index cf77005f3c391fdd47a8f967520425ed4c88ab63..47b2f8300d553d6ba944c1309ec5c233ad1f4951 100644 (file)
--- a/htsworkflow/pipelines/fastq.py
+++ b/htsworkflow/pipelines/fastq.py
@@ -40,5 +40,6 @@ def summarize_hiseq_fastq(stream):
 
 if __name__ == '__main__':
     import sys
 
 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)
         print summarize_hiseq_fastq(instream)