| ANALYSIS_NAME | broad.pda.seq.rap.CollectAnnotationEnrichments | |
| ANNOTATION | broad.pda.seq.rap.GenomeCommandLineProgram | |
| ANNOTATION_BASE | broad.pda.seq.rap.CollectAnnotationEnrichments | |
| ANNOTATIONS | broad.pda.seq.rap.CollectAnnotationEnrichments | |
| BAM_EXTENSION | broad.pda.seq.rap.CollectAnnotationEnrichments | |
| calculateBamEnrichments(AnnotationList< Annotation > regions, AnnotationList< Annotation > peaks, SortedMap< String, File > bamMap) | broad.pda.seq.rap.CollectAnnotationEnrichments | protected |
| calculateDiscreteAnnotationEnrichments(AnnotationList< Annotation > regions, AnnotationList< Annotation > peaks, SortedMap< String, File > discreteAnnotations) | broad.pda.seq.rap.CollectAnnotationEnrichments | protected |
| cleanup(SortedMap< String, File > discreteAnnotations) | broad.pda.seq.rap.CollectAnnotationEnrichments | protected |
| collectResults(SortedMap< String, File > discreteAnnotations) | broad.pda.seq.rap.CollectAnnotationEnrichments | protected |
| CONTINUOUS_EXTENSION | broad.pda.seq.rap.CollectAnnotationEnrichments | |
| COORD_SPACE | broad.pda.seq.rap.GenomeCommandLineProgram | |
| coordinateSpace | broad.pda.seq.rap.GenomeCommandLineProgram | protected |
| customCommandLineValidation() | broad.pda.seq.rap.CollectAnnotationEnrichments | protected |
| DISCRETE_EXTENSION | broad.pda.seq.rap.CollectAnnotationEnrichments | |
| doWork() | broad.pda.seq.rap.CollectAnnotationEnrichments | protected |
| GENE | broad.pda.seq.rap.GenomeCommandLineProgram | |
| getCoordinateSpace() | broad.pda.seq.rap.GenomeCommandLineProgram | protected |
| getGenes() | broad.pda.seq.rap.GenomeCommandLineProgram | |
| getPeakScores(AnnotationList< Annotation > regions, AnnotationList<?extends Annotation > peaks, AnnotationCollection<?extends Annotation > annotations) | broad.pda.seq.rap.CollectAnnotationEnrichments | protected |
| getRegions() | broad.pda.seq.rap.GenomeCommandLineProgram | |
| getRegionSet() | broad.pda.seq.rap.GenomeCommandLineProgram | |
| getRegionsMap() | broad.pda.seq.rap.GenomeCommandLineProgram | |
| INPUT | broad.pda.seq.rap.CollectAnnotationEnrichments | |
| isGenomicSpace() | broad.pda.seq.rap.GenomeCommandLineProgram | |
| KEEP_INTERMEDIATES | broad.pda.seq.rap.CollectAnnotationEnrichments | |
| loadAlignmentModel(File bamFile) | broad.pda.seq.rap.GenomeCommandLineProgram | |
| loadAlignmentModel(File bamFile, boolean pairedEnd) | broad.pda.seq.rap.GenomeCommandLineProgram | |
| loadCoordinateSpace() | broad.pda.seq.rap.GenomeCommandLineProgram | protected |
| main(final String[] args) | broad.pda.seq.rap.CollectAnnotationEnrichments | static |
| MASK_FILE | broad.pda.seq.rap.GenomeCommandLineProgram | |
| MAX_FRAGMENT_LENGTH | broad.pda.seq.rap.GenomeCommandLineProgram | |
| MIN_MAPPING_QUALITY | broad.pda.seq.rap.GenomeCommandLineProgram | |
| OUTPUT | broad.pda.seq.rap.CollectAnnotationEnrichments | |
| PAIRED_END | broad.pda.seq.rap.CollectAnnotationEnrichments | |
| PCT_MASKED_ALLOWED | broad.pda.seq.rap.GenomeCommandLineProgram | |
| PERMUTATIONS | broad.pda.seq.rap.CollectAnnotationEnrichments | |
| PERMUTE | broad.pda.seq.rap.CollectAnnotationEnrichments | |
| processOneAnnotationSet(String name, AnnotationList< Annotation > regions, AnnotationList< Annotation > peaks, AnnotationCollection<?extends Annotation > annotations) | broad.pda.seq.rap.CollectAnnotationEnrichments | protected |
| QUEUE | broad.pda.seq.rap.CollectAnnotationEnrichments | |
| REGION | broad.pda.seq.rap.GenomeCommandLineProgram | |
| shufflePeaks(AnnotationList< Annotation > regions, AnnotationList< Annotation > peaks, String output) | broad.pda.seq.rap.CollectAnnotationEnrichments | protected |
| SIZES | broad.pda.seq.rap.GenomeCommandLineProgram | |
| submitJobs(SortedMap< String, File > annotationMap) | broad.pda.seq.rap.CollectAnnotationEnrichments | protected |
| USAGE | broad.pda.seq.rap.CollectAnnotationEnrichments | |
1.8.7
