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comparison unified_genotyper.xml @ 33:76f8ca47b810 draft

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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
comparison
equal deleted inserted replaced
32:fd9d089a9ff4 33:76f8ca47b810
50 #end for 50 #end for
51 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: 51 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
52 -p '--pedigreeString "${pedigree_string.pedigree_string}"' 52 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
53 #end for 53 #end for
54 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' 54 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
55 #set default_read_filters = ['DuplicateReadFilter', 'FailsVendorQualityCheckFilter', 'NotPrimaryAlignmentFilter', 'MalformedReadFilter', 'BadMateFilter', 'MappingQualityUnavailableFilter', 'UnmappedReadFilter']
55 #for $read_filter in $gatk_param_type.read_filter: 56 #for $read_filter in $gatk_param_type.read_filter:
56 -p ' 57 -p '
57 #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: 58 #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters:
58 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" 59 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
59 #end_if 60 #end_if
60 ###raise Exception( str( dir( $read_filter ) ) )
61 #for $name, $param in $read_filter.read_filter_type.iteritems(): 61 #for $name, $param in $read_filter.read_filter_type.iteritems():
62 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: 62 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
63 #if hasattr( $param.input, 'truevalue' ): 63 #if hasattr( $param.input, 'truevalue' ):
64 ${param} 64 ${param}
65 #else: 65 #else: