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comparison depth_of_coverage.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 6ef8eb568700
children b99c25b0ad4d
comparison
equal deleted inserted replaced
32:fd9d089a9ff4 33:76f8ca47b810
46 #end for 46 #end for
47 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat: 47 #for $pedigree_string in $gatk_param_type.pedigree_string_repeat:
48 -p '--pedigreeString "${pedigree_string.pedigree_string}"' 48 -p '--pedigreeString "${pedigree_string.pedigree_string}"'
49 #end for 49 #end for
50 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"' 50 -p '--pedigreeValidationType "${gatk_param_type.pedigree_validation_type}"'
51 #set default_read_filters = ['DuplicateReadFilter','FailsVendorQualityCheckFilter','NotPrimaryAlignmentFilter','MalformedReadFilter','UnmappedReadFilter']
51 #for $read_filter in $gatk_param_type.read_filter: 52 #for $read_filter in $gatk_param_type.read_filter:
52 -p '--read_filter "${read_filter.read_filter_type.read_filter_type_selector}" 53 -p '
54 #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters:
55 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}"
56 #end_if
53 ###raise Exception( str( dir( $read_filter ) ) ) 57 ###raise Exception( str( dir( $read_filter ) ) )
54 #for $name, $param in $read_filter.read_filter_type.iteritems(): 58 #for $name, $param in $read_filter.read_filter_type.iteritems():
55 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: 59 #if $name not in [ "__current_case__", "read_filter_type_selector" ]:
56 #if hasattr( $param.input, 'truevalue' ): 60 #if hasattr( $param.input, 'truevalue' ):
57 ${param} 61 ${param}