# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1362145922 21600
# Node ID a29c7d7d962d7dd91d95f6f311cdb15efe582049
# Parent  b99c25b0ad4d0e3056833eac3b233c9995e54952
Fix default read filter screening

diff -r b99c25b0ad4d -r a29c7d7d962d base_recalibrator.xml
--- a/base_recalibrator.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/base_recalibrator.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -61,8 +61,12 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+        #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MappingQualityZero','MalformedRead','MappingQualityUnavailable','UnmappedRead']
         #for $read_filter in $gatk_param_type.read_filter:
-            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
+            -p '
+            #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
             ###raise Exception( str( dir( $read_filter ) ) )
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
@@ -284,7 +288,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d depth_of_coverage.xml
--- a/depth_of_coverage.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/depth_of_coverage.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -48,10 +48,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
+        #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','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
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -295,7 +295,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d haplotype_caller.xml
--- a/haplotype_caller.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/haplotype_caller.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -36,8 +36,12 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+        #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead']
         #for $read_filter in $gatk_param_type.read_filter:
-            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
+            -p '
+            #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
             ###raise Exception( str( dir( $read_filter ) ) )
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
@@ -273,7 +277,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d indel_realigner.xml
--- a/indel_realigner.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/indel_realigner.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -47,10 +47,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['MalformedReadFilter']
+        #set default_read_filters = ['MalformedRead']
         #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
             ###raise Exception( str( dir( $read_filter ) ) )
@@ -236,7 +236,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d print_reads.xml
--- a/print_reads.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/print_reads.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -37,10 +37,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['MalformedReadFilter']
+        #set default_read_filters = ['MalformedRead']
         #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 $read_filter.read_filter_type.iteritems():
@@ -216,7 +216,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d realigner_target_creator.xml
--- a/realigner_target_creator.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/realigner_target_creator.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -44,10 +44,10 @@
             -p '--pedigreeString "${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 $read_filter.read_filter_type.iteritems():
@@ -221,7 +221,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d reduce_reads.xml
--- a/reduce_reads.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/reduce_reads.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -37,10 +37,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['MalformedReadFilter']
+        #set default_read_filters = ['MalformedRead']
         #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 $read_filter.read_filter_type.iteritems():
@@ -221,7 +221,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d unified_genotyper.xml
--- a/unified_genotyper.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/unified_genotyper.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -5,7 +5,6 @@
       <requirement type="package" version="0.1.18">samtools</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
-   #set default_read_filters = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'BadMateFilter', 'MappingQualityUnavailableFilter', 'UnmappedReadFilter'] 
    --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
    #for $i, $input_bam in enumerate( $reference_source.input_bams ):
@@ -52,10 +51,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'BadMateFilter', 'MappingQualityUnavailableFilter', 'UnmappedReadFilter']
+        #set default_read_filters = ['DuplicateRead', 'FailsVendorQualityCheck', 'NotPrimaryAlignment', 'MalformedRead', 'BadMate', '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 $read_filter.read_filter_type.iteritems():
@@ -282,7 +281,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d variant_annotator.xml
--- a/variant_annotator.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/variant_annotator.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -82,10 +82,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
+        #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','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 $read_filter.read_filter_type.iteritems():
@@ -302,7 +302,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d variant_apply_recalibration.xml
--- a/variant_apply_recalibration.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/variant_apply_recalibration.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -33,10 +33,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
+        #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','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 $read_filter.read_filter_type.iteritems():
@@ -192,7 +192,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d variant_combine.xml
--- a/variant_combine.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/variant_combine.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -39,10 +39,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
+        #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','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 $read_filter.read_filter_type.iteritems():
@@ -212,7 +212,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d variant_eval.xml
--- a/variant_eval.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/variant_eval.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -47,10 +47,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
+        #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','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 $read_filter.read_filter_type.iteritems():
@@ -268,7 +268,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d variant_filtration.xml
--- a/variant_filtration.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/variant_filtration.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -43,10 +43,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
+        #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','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 $read_filter.read_filter_type.iteritems():
@@ -221,7 +221,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d variant_recalibrator.xml
--- a/variant_recalibrator.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/variant_recalibrator.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -51,10 +51,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
+        #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','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 $read_filter.read_filter_type.iteritems():
@@ -447,7 +447,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d variant_select.xml
--- a/variant_select.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/variant_select.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -103,10 +103,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
+        #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','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 $read_filter.read_filter_type.iteritems():
@@ -266,7 +266,7 @@
                   <!-- no extra options -->
               </when>
               <when value="MalformedRead">
-                  <!-- no extra options -->
+                  <param name="filter_mismatching_base_and_quals" type="boolean" truevalue="--filter_mismatching_base_and_quals" falsevalue="" checked="false" label="filter out the reads with mismatching number of bases and base qualities" help="filter out the mismatch reads instead of quitting with an error"/>
               </when>
               <when value="MappingQuality">
                   <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/>
diff -r b99c25b0ad4d -r a29c7d7d962d variants_validate.xml
--- a/variants_validate.xml	Thu Feb 28 15:41:24 2013 -0600
+++ b/variants_validate.xml	Fri Mar 01 07:52:02 2013 -0600
@@ -36,10 +36,10 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
-        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
+        #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','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():
@@ -192,7 +192,7 @@
                   <!-- 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"/>