details: http://www.bx.psu.edu/hg/galaxy/rev/7fd7bbe91838 changeset: 2874:7fd7bbe91838 user: Kelly Vincent <kpvincent@bx.psu.edu> date: Mon Oct 12 14:40:01 2009 -0400 description: Corrected Bowtie wrapper's output type (to SAM) for one missed condition, and also corrected problem with handling of full parameter list 1 file(s) affected in this change: tools/sr_mapping/bowtie_wrapper.py diffs (21 lines): diff -r 4a3e48e1e8e1 -r 7fd7bbe91838 tools/sr_mapping/bowtie_wrapper.py --- a/tools/sr_mapping/bowtie_wrapper.py Mon Oct 12 14:04:28 2009 -0400 +++ b/tools/sr_mapping/bowtie_wrapper.py Mon Oct 12 14:40:01 2009 -0400 @@ -119,7 +119,7 @@ ('','-I %s'%options.minInsert)[options.minInsert!='None'], ('','-X %s'%options.maxInsert)[options.maxInsert!='None'], ('','--%s'%options.mateOrient)[options.mateOrient!='None'], - ('','--pairtries %s'%options.maxAlignAttempt)[int(options.maxAlignAttempt)>=0], + ('','--pairtries %s'%options.maxAlignAttempt)[options.maxAlignAttempt!='None' and int(options.maxAlignAttempt)>=0], ('','--nofw')[options.forwardAlign=='noForward'], ('','--norc')[options.reverseAlign=='noReverse'], ('','--maxbts %s'%options.maxBacktracks)[options.maxBacktracks!='None' and (options.mismatchSeed=='2' or options.mismatchSeed=='3')], @@ -133,7 +133,7 @@ ('','--seed %s'%options.seed)[int(options.seed)>=0], options.threads) except ValueError: - aligning_cmds = '-p %s' % options.threads + aligning_cmds = '-p %s -S' % options.threads # prepare actual aligning commands if options.paired == 'paired':