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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}"