# HG changeset patch
# User devteam
# Date 1421354224 18000
# Node ID 4ff1e04010e62da3ae9a25c1ed950be4fef2ccd7
# Parent  3d4f1fa26f0ef80dbf33feeaf5d72dc5773dd672
Uploaded

diff -r 3d4f1fa26f0e -r 4ff1e04010e6 picard_EstimateLibraryComplexity.xml
--- 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}"
diff -r 3d4f1fa26f0e -r 4ff1e04010e6 picard_MarkDuplicates.xml
--- 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}"
diff -r 3d4f1fa26f0e -r 4ff1e04010e6 picard_MarkDuplicatesWithMateCigar.xml
--- 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}"