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comparison picard_MarkDuplicates.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
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