Mercurial > repos > devteam > picard
comparison picard_MarkDuplicatesWithMateCigar.xml @ 6:4ff1e04010e6 draft
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| author | devteam |
|---|---|
| date | Thu, 15 Jan 2015 15:37:04 -0500 |
| parents | 3d4f1fa26f0e |
| children | 3a3234d7a2e8 |
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| 5:3d4f1fa26f0e | 6:4ff1e04010e6 |
|---|---|
| 29 REMOVE_DUPLICATES="${remove_duplicates}" | 29 REMOVE_DUPLICATES="${remove_duplicates}" |
| 30 ASSUME_SORTED="${assume_sorted}" | 30 ASSUME_SORTED="${assume_sorted}" |
| 31 | 31 |
| 32 DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" | 32 DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" |
| 33 | 33 |
| 34 READ_NAME_REGEX="${read_name_regex}" | 34 #import pipes |
| 35 READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } | |
| 35 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" | 36 OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" |
| 36 | 37 |
| 37 | 38 |
| 38 BLOCK_SIZE=100000 | 39 BLOCK_SIZE=100000 |
| 39 VALIDATION_STRINGENCY="${validation_stringency}" | 40 VALIDATION_STRINGENCY="${validation_stringency}" |