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root/gclib/tophat_cpp/tophat
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# Line 1494 | Line 1494
1494                           "-k", str(params.max_hits),
1495                           "-m", str(params.max_hits),
1496                           "--max", "/dev/null",
1497 <                         "--sam-nohead"]
1497 >                         "--sam-nohead"] #always use headerless SAM file
1498          fix_map_cmd = [prog_path('fix_map_ordering')]
1499          sam_zipcmd=None
1500          if unmapped_reads:

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