Mercurial > repos > mzeidler > virana_main
comparison vmap.py @ 9:be5d3889a1b9 draft
Uploaded
| author | mzeidler |
|---|---|
| date | Thu, 26 Sep 2013 07:23:48 -0400 |
| parents | f63d639b223c |
| children |
comparison
equal
deleted
inserted
replaced
| 8:0d0b19f1b740 | 9:be5d3889a1b9 |
|---|---|
| 1076 '--outSAMmode', 'Full', | 1076 '--outSAMmode', 'Full', |
| 1077 '--outSAMstrandField', 'None', | 1077 '--outSAMstrandField', 'None', |
| 1078 '--outSAMattributes', 'Standard', | 1078 '--outSAMattributes', 'Standard', |
| 1079 '--outSAMunmapped', 'Within', | 1079 '--outSAMunmapped', 'Within', |
| 1080 '--outStd', 'SAM', | 1080 '--outStd', 'SAM', |
| 1081 '--outFilterMultimapNmax', '1000', | 1081 '--outFilterMultimapNmax', '1000'] |
| 1082 '--outSAMprimaryFlag', 'AllBestScore', | |
| 1083 '--outSAMorder', 'PairedKeepInputOrder'] | |
| 1084 | 1082 |
| 1085 if self.unmapped1 or self.unmapped2: | 1083 if self.unmapped1 or self.unmapped2: |
| 1086 star_cline += ['--outReadsUnmapped', 'Fastx'] | 1084 star_cline += ['--outReadsUnmapped', 'Fastx'] |
| 1087 else: | 1085 else: |
| 1088 star_cline += ['--outReadsUnmapped', 'None'] | 1086 star_cline += ['--outReadsUnmapped', 'None'] |