diff variant_recalibrator.xml @ 33:76f8ca47b810 draft

Omit --read_filter param included by default

--- 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' ):