Mercurial > repos > jjohnson > gatk2
comparison depth_of_coverage.xml @ 35:a29c7d7d962d draft
Fix default read filter screening
| author | Jim Johnson <jj@umn.edu> |
|---|---|
| date | Fri, 01 Mar 2013 07:52:02 -0600 |
| parents | b99c25b0ad4d |
| children | 14d47237bb0a |
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| 34:b99c25b0ad4d | 35:a29c7d7d962d |
|---|---|
| 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 #set default_read_filters = ['DuplicateRead','FailsVendorQualityCheck','NotPrimaryAlignment','MalformedRead','UnmappedRead'] |
| 52 #for $read_filter in $gatk_param_type.read_filter: | 52 #for $read_filter in $gatk_param_type.read_filter: |
| 53 -p ' | 53 -p ' |
| 54 #if ${read_filter.read_filter_type.read_filter_type_selector} not in $default_read_filters: | 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}" | 55 --read_filter "${read_filter.read_filter_type.read_filter_type_selector}" |
| 56 #end_if | 56 #end_if |
| 57 ###raise Exception( str( dir( $read_filter ) ) ) | 57 ###raise Exception( str( dir( $read_filter ) ) ) |
| 58 #for $name, $param in $read_filter.read_filter_type.iteritems(): | 58 #for $name, $param in $read_filter.read_filter_type.iteritems(): |
| 59 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: | 59 #if $name not in [ "__current_case__", "read_filter_type_selector" ]: |
| 293 </when> | 293 </when> |
| 294 <when value="FailsVendorQualityCheck"> | 294 <when value="FailsVendorQualityCheck"> |
| 295 <!-- no extra options --> | 295 <!-- no extra options --> |
| 296 </when> | 296 </when> |
| 297 <when value="MalformedRead"> | 297 <when value="MalformedRead"> |
| 298 <!-- no extra options --> | 298 <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"/> |
| 299 </when> | 299 </when> |
| 300 <when value="MappingQuality"> | 300 <when value="MappingQuality"> |
| 301 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> | 301 <param name="min_mapping_quality_score" type="integer" value="10" label="Minimum read mapping quality required to consider a read for calling"/> |
| 302 </when> | 302 </when> |
| 303 <when value="MappingQualityUnavailable"> | 303 <when value="MappingQualityUnavailable"> |