Mercurial > repos > devteam > picard
comparison picard_MarkDuplicates.xml @ 6:4ff1e04010e6 draft
Uploaded
| author | devteam |
|---|---|
| date | Thu, 15 Jan 2015 15:37:04 -0500 |
| parents | 3d4f1fa26f0e |
| children | 3a3234d7a2e8 |
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| 5:3d4f1fa26f0e | 6:4ff1e04010e6 |
|---|---|
| 24 REMOVE_DUPLICATES="${remove_duplicates}" | 24 REMOVE_DUPLICATES="${remove_duplicates}" |
| 25 ASSUME_SORTED="${assume_sorted}" | 25 ASSUME_SORTED="${assume_sorted}" |
| 26 | 26 |
| 27 DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" | 27 DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" |
| 28 | 28 |
| 29 READ_NAME_REGEX="${read_name_regex}" | 29 #import pipes |
| 30 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } | |
| 30 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" | 31 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" |
| 31 | 32 |
| 32 VALIDATION_STRINGENCY="${validation_stringency}" | 33 VALIDATION_STRINGENCY="${validation_stringency}" |
| 33 QUIET=true | 34 QUIET=true |
| 34 VERBOSITY=ERROR | 35 VERBOSITY=ERROR |