diff unified_genotyper.xml @ 35:a29c7d7d962d draft

Fix default read filter screening

--- 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"/>