diff realigner_target_creator.xml @ 35:a29c7d7d962d draft

Fix default read filter screening

--- a/realigner_target_creator.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/realigner_target_creator.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -44,10 +44,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MappingQualityZeroFilter','MalformedReadFilter','BadCigarFilter','BadMateFilter','Platform454Filter','MappingQualityUnavailableFilter','UnmappedReadFilter']
+        #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MappingQualityZero','MalformedRead','BadCigar','BadMate','Platform454','MappingQualityUnavailable','UnmappedRead']
         #for $read_filter in $gatk_param_type.read_filter:
             -p '
-            #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters:
+            #if $read_filter.read_filter_type.read_filter_type_selector not in $default_read_filters:
                 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
             #end_if
             #for $name, $param in $read_filter.read_filter_type.iteritems():
@@ -221,7 +221,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>