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diff 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
line wrap: on
line diff
--- 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}"