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 f180f47c7c6ac3aabf0530067a0a25d195b773b7..b21353a12b432621d4f7b53ea0fb76f566b73c26 100755 (executable)
--- 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