# HG changeset patch
# User Jim Johnson <jj@umn.edu>
# Date 1362087124 21600
# Node ID 76f8ca47b810a0af6aed296669bca7aae2bfeeb4
# Parent  fd9d089a9ff41af7ee8b086557762c52b333a56b
Omit --read_filter param included by default

diff -r fd9d089a9ff4 -r 76f8ca47b810 depth_of_coverage.xml
--- a/depth_of_coverage.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/depth_of_coverage.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -48,8 +48,12 @@
             -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']
         #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 $name not in [ "__current_case__", "read_filter_type_selector" ]:
diff -r fd9d089a9ff4 -r 76f8ca47b810 indel_realigner.xml
--- a/indel_realigner.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/indel_realigner.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -47,8 +47,12 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+        #set default_read_filters = ['MalformedReadFilter']
         #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 $name not in [ "__current_case__", "read_filter_type_selector" ]:
diff -r fd9d089a9ff4 -r 76f8ca47b810 print_reads.xml
--- a/print_reads.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/print_reads.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -37,9 +37,12 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+        #set default_read_filters = ['MalformedReadFilter']
         #for $read_filter in $gatk_param_type.read_filter:
-            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            ###raise Exception( str( dir( $read_filter ) ) )
+            -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
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r fd9d089a9ff4 -r 76f8ca47b810 realigner_target_creator.xml
--- a/realigner_target_creator.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/realigner_target_creator.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -44,9 +44,12 @@
             -p '--pedigreeString "${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']
         #for $read_filter in $gatk_param_type.read_filter:
-            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            ###raise Exception( str( dir( $read_filter ) ) )
+            -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
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r fd9d089a9ff4 -r 76f8ca47b810 reduce_reads.xml
--- a/reduce_reads.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/reduce_reads.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -37,9 +37,12 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+        #set default_read_filters = ['MalformedReadFilter']
         #for $read_filter in $gatk_param_type.read_filter:
-            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            ###raise Exception( str( dir( $read_filter ) ) )
+            -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
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r fd9d089a9ff4 -r 76f8ca47b810 unified_genotyper.xml
--- a/unified_genotyper.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/unified_genotyper.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -52,12 +52,12 @@
             -p '--pedigreeString "${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']
         #for $read_filter in $gatk_param_type.read_filter:
             -p '
             #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters:
-              --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
+                --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" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r fd9d089a9ff4 -r 76f8ca47b810 variant_annotator.xml
--- a/variant_annotator.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/variant_annotator.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -82,9 +82,12 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
         #for $read_filter in $gatk_param_type.read_filter:
-            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            ###raise Exception( str( dir( $read_filter ) ) )
+            -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
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r fd9d089a9ff4 -r 76f8ca47b810 variant_apply_recalibration.xml
--- a/variant_apply_recalibration.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/variant_apply_recalibration.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -33,9 +33,12 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
         #for $read_filter in $gatk_param_type.read_filter:
-            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            ###raise Exception( str( dir( $read_filter ) ) )
+            -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
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r fd9d089a9ff4 -r 76f8ca47b810 variant_combine.xml
--- a/variant_combine.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/variant_combine.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -39,9 +39,12 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
         #for $read_filter in $gatk_param_type.read_filter:
-            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            ###raise Exception( str( dir( $read_filter ) ) )
+            -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
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r fd9d089a9ff4 -r 76f8ca47b810 variant_eval.xml
--- a/variant_eval.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/variant_eval.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -47,9 +47,12 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
         #for $read_filter in $gatk_param_type.read_filter:
-            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            ###raise Exception( str( dir( $read_filter ) ) )
+            -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
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r fd9d089a9ff4 -r 76f8ca47b810 variant_filtration.xml
--- a/variant_filtration.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/variant_filtration.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -43,9 +43,12 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
         #for $read_filter in $gatk_param_type.read_filter:
-            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            ###raise Exception( str( dir( $read_filter ) ) )
+            -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
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r fd9d089a9ff4 -r 76f8ca47b810 variant_recalibrator.xml
--- a/variant_recalibrator.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/variant_recalibrator.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -4,7 +4,6 @@
       <requirement type="package" version="2.3">gatk</requirement>
   </requirements>
   <command interpreter="python">gatk2_wrapper.py
-   #set default_read_filters = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'UnmappedReadFilter']
    --max_jvm_heap_fraction "1"
    --stdout "${output_log}"
    #for $var_count, $variant in enumerate( $reference_source.variants ):
@@ -52,12 +51,12 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
         #for $read_filter in $gatk_param_type.read_filter:
             -p '
             #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters:
-              --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
+                --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" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r fd9d089a9ff4 -r 76f8ca47b810 variant_select.xml
--- a/variant_select.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/variant_select.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -103,9 +103,12 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
         #for $read_filter in $gatk_param_type.read_filter:
-            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            ###raise Exception( str( dir( $read_filter ) ) )
+            -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
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):
diff -r fd9d089a9ff4 -r 76f8ca47b810 variants_validate.xml
--- a/variants_validate.xml	Thu Feb 28 12:45:44 2013 -0600
+++ b/variants_validate.xml	Thu Feb 28 15:32:04 2013 -0600
@@ -36,9 +36,12 @@
             -p '--pedigreeString "${pedigree_string.pedigree_string}"'
         #end for
         -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
+        #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
         #for $read_filter in $gatk_param_type.read_filter:
-            -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
-            ###raise Exception( str( dir( $read_filter ) ) )
+            -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
             #for $name, $param in $read_filter.read_filter_type.iteritems():
                 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
                     #if hasattr( $param.input, 'truevalue' ):