Mercurial > repos > devteam > picard
changeset 6:4ff1e04010e6 draft
Uploaded
| author | devteam |
|---|---|
| date | Thu, 15 Jan 2015 15:37:04 -0500 |
| parents | 3d4f1fa26f0e |
| children | 379fdf4c41ac |
| files | picard_EstimateLibraryComplexity.xml picard_MarkDuplicates.xml picard_MarkDuplicatesWithMateCigar.xml |
| diffstat | 3 files changed, 6 insertions(+), 3 deletions(-) [+] |
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--- a/picard_EstimateLibraryComplexity.xml Tue Dec 16 19:03:21 2014 -0500 +++ b/picard_EstimateLibraryComplexity.xml Thu Jan 15 15:37:04 2015 -0500 @@ -21,7 +21,8 @@ MAX_DIFF_RATE="${max_diff_rate}" MIN_MEAN_QUALITY="${min_mean_quality}" MAX_GROUP_RATIO="${max_group_ratio}" - READ_NAME_REGEX="${read_name_regex}" + #import pipes + READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" VALIDATION_STRINGENCY="${validation_stringency}"
--- a/picard_MarkDuplicates.xml Tue Dec 16 19:03:21 2014 -0500 +++ b/picard_MarkDuplicates.xml Thu Jan 15 15:37:04 2015 -0500 @@ -26,7 +26,8 @@ DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" - READ_NAME_REGEX="${read_name_regex}" + #import pipes + READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}" VALIDATION_STRINGENCY="${validation_stringency}"
--- a/picard_MarkDuplicatesWithMateCigar.xml Tue Dec 16 19:03:21 2014 -0500 +++ b/picard_MarkDuplicatesWithMateCigar.xml Thu Jan 15 15:37:04 2015 -0500 @@ -31,7 +31,8 @@ DUPLICATE_SCORING_STRATEGY="${duplicate_scoring_strategy}" - READ_NAME_REGEX="${read_name_regex}" + #import pipes + READ_NAME_REGEX=${ pipes.quote( str( $read_name_regex ) ) or "''" } OPTICAL_DUPLICATE_PIXEL_DISTANCE="${optical_duplicate_pixel_distance}"