Mercurial > repos > jjohnson > gatk2
comparison variant_annotator.xml @ 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 | 6ef8eb568700 |
| children | b99c25b0ad4d |
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| 32:fd9d089a9ff4 | 33:76f8ca47b810 |
|---|---|
| 80 #end for | 80 #end for |
| 81 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: | 81 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: |
| 82 -p '--pedigreeString "${pedigree_string.pedigree_string}"' | 82 -p '--pedigreeString "${pedigree_string.pedigree_string}"' |
| 83 #end for | 83 #end for |
| 84 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' | 84 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' |
| 85 #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter'] | |
| 85 #for $read_filter in $gatk_param_type.read_filter: | 86 #for $read_filter in $gatk_param_type.read_filter: |
| 86 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" | 87 -p ' |
| 87 ###raise Exception( str( dir( $read_filter ) ) ) | 88 #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: |
| 89 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" | |
| 90 #end_if | |
| 88 #for $name, $param in $read_filter.read_filter_type.iteritems(): | 91 #for $name, $param in $read_filter.read_filter_type.iteritems(): |
| 89 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: | 92 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: |
| 90 #if hasattr( $param.input, 'truevalue' ): | 93 #if hasattr( $param.input, 'truevalue' ): |
| 91 ${param} | 94 ${param} |
| 92 #else: | 95 #else: |