From: Diane Trout <diane@caltech.edu>
Date: Fri, 9 Jul 2010 00:08:12 +0000 (+0000)
Subject: Since srf2named_fastq detects what type of srf file I can remove
X-Git-Tag: 0.4.4~8
X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=htsworkflow.git;a=commitdiff_plain;h=057ecb2692be78219b92c8f3b48ec5555e81fa64

Since srf2named_fastq detects what type of srf file I can remove
the -c option that was forcing it to read CNF1 formatted srf files
---

diff --git a/extra/ucsc_encode_submission/ucsc_gather.py b/extra/ucsc_encode_submission/ucsc_gather.py
index f180f47..b21353a 100755
--- a/extra/ucsc_encode_submission/ucsc_gather.py
+++ b/extra/ucsc_encode_submission/ucsc_gather.py
@@ -518,7 +518,7 @@ def get_library_info(host, apidata, library_id):
 
 def condor_srf_to_fastq(srf_file, target_pathname, paired, flowcell=None,
                         mid=None, force=False):
-    args = ['-c', srf_file, ]
+    args = [ srf_file, ]
     if paired:
         args.extend(['--left', target_pathname])
         # this is ugly. I did it because I was pregenerating the target