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comparison picard_FastqToSam.xml @ 3:bf1c3f9f8282

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Fix for FastqToSam MAX_Q usage detection.
author Daniel Blankenberg <dan@bx.psu.edu>
date Fri, 03 May 2013 17:13:01 -0400
parents 1cd7f3b42609
children 3d4f1fa26f0e
comparison
equal deleted inserted replaced
2:9227b8c3093b 3:bf1c3f9f8282
35 RUN_DATE="${param_type.run_date}" 35 RUN_DATE="${param_type.run_date}"
36 #end if 36 #end if
37 #if str( $param_type.min_q ) != "": 37 #if str( $param_type.min_q ) != "":
38 MIN_Q="${param_type.min_q}" 38 MIN_Q="${param_type.min_q}"
39 #end if 39 #end if
40 #if str( $param_type.min_q ) != "": 40 #if str( $param_type.max_q ) != "":
41 MAX_Q="${param_type.max_q}" 41 MAX_Q="${param_type.max_q}"
42 #end if 42 #end if
43 SORT_ORDER="${param_type.sort_order}" 43 SORT_ORDER="${param_type.sort_order}"
44 #else: 44 #else:
45 SORT_ORDER=coordinate ##unsorted, queryname, coordinate; always use coordinate 45 SORT_ORDER=coordinate ##unsorted, queryname, coordinate; always use coordinate