Mercurial > repos > jjohnson > gatk2
changeset 33:76f8ca47b810 draft
Omit --read_filter param included by default
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Thu, 28 Feb 2013 15:32:04 -0600 |
| parents | fd9d089a9ff4 |
| children | b99c25b0ad4d |
| files | depth_of_coverage.xml indel_realigner.xml print_reads.xml realigner_target_creator.xml reduce_reads.xml unified_genotyper.xml variant_annotator.xml variant_apply_recalibration.xml variant_combine.xml variant_eval.xml variant_filtration.xml variant_recalibrator.xml variant_select.xml variants_validate.xml |
| diffstat | 14 files changed, 64 insertions(+), 27 deletions(-) [+] |
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--- 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 $name not in [ "__current_case__", "read_filter_type_selector" ]:
--- a/indel_realigner.xml Thu Feb 28 12:45:44 2013 -0600 +++ b/indel_realigner.xml Thu Feb 28 15:32:04 2013 -0600 @@ -47,8 +47,12 @@ -p '--pedigreeString "${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 $name not in [ "__current_case__", "read_filter_type_selector" ]:
--- a/print_reads.xml Thu Feb 28 12:45:44 2013 -0600 +++ b/print_reads.xml Thu Feb 28 15:32:04 2013 -0600 @@ -37,9 +37,12 @@ -p '--pedigreeString "${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( $param.input, 'truevalue' ):
--- a/realigner_target_creator.xml Thu Feb 28 12:45:44 2013 -0600 +++ b/realigner_target_creator.xml Thu Feb 28 15:32:04 2013 -0600 @@ -44,9 +44,12 @@ -p '--pedigreeString "${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( $param.input, 'truevalue' ):
--- a/reduce_reads.xml Thu Feb 28 12:45:44 2013 -0600 +++ b/reduce_reads.xml Thu Feb 28 15:32:04 2013 -0600 @@ -37,9 +37,12 @@ -p '--pedigreeString "${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( $param.input, 'truevalue' ):
--- a/unified_genotyper.xml Thu Feb 28 12:45:44 2013 -0600 +++ b/unified_genotyper.xml Thu Feb 28 15:32:04 2013 -0600 @@ -52,12 +52,12 @@ -p '--pedigreeString "${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( $param.input, 'truevalue' ):
--- a/variant_annotator.xml Thu Feb 28 12:45:44 2013 -0600 +++ b/variant_annotator.xml Thu Feb 28 15:32:04 2013 -0600 @@ -82,9 +82,12 @@ -p '--pedigreeString "${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( $param.input, 'truevalue' ):
--- a/variant_apply_recalibration.xml Thu Feb 28 12:45:44 2013 -0600 +++ b/variant_apply_recalibration.xml Thu Feb 28 15:32:04 2013 -0600 @@ -33,9 +33,12 @@ -p '--pedigreeString "${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( $param.input, 'truevalue' ):
--- a/variant_combine.xml Thu Feb 28 12:45:44 2013 -0600 +++ b/variant_combine.xml Thu Feb 28 15:32:04 2013 -0600 @@ -39,9 +39,12 @@ -p '--pedigreeString "${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( $param.input, 'truevalue' ):
--- a/variant_eval.xml Thu Feb 28 12:45:44 2013 -0600 +++ b/variant_eval.xml Thu Feb 28 15:32:04 2013 -0600 @@ -47,9 +47,12 @@ -p '--pedigreeString "${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( $param.input, 'truevalue' ):
--- a/variant_filtration.xml Thu Feb 28 12:45:44 2013 -0600 +++ b/variant_filtration.xml Thu Feb 28 15:32:04 2013 -0600 @@ -43,9 +43,12 @@ -p '--pedigreeString "${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( $param.input, 'truevalue' ):
--- a/variant_recalibrator.xml Thu Feb 28 12:45:44 2013 -0600 +++ b/variant_recalibrator.xml Thu Feb 28 15:32:04 2013 -0600 @@ -4,7 +4,6 @@ <requirement type="package" version="2.3">gatk</requirement> </requirements> <command interpreter="python">gatk2_wrapper.py - #set default_read_filters = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'UnmappedReadFilter'] --max_jvm_heap_fraction "1" --stdout "${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( $param.input, 'truevalue' ):
--- a/variant_select.xml Thu Feb 28 12:45:44 2013 -0600 +++ b/variant_select.xml Thu Feb 28 15:32:04 2013 -0600 @@ -103,9 +103,12 @@ -p '--pedigreeString "${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( $param.input, 'truevalue' ):
--- a/variants_validate.xml Thu Feb 28 12:45:44 2013 -0600 +++ b/variants_validate.xml Thu Feb 28 15:32:04 2013 -0600 @@ -36,9 +36,12 @@ -p '--pedigreeString "${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' ):