| calculatePVal(int k, double lambda, double w, double T) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | static |
| ContinuousDataAlignmentModel(AlignmentDataModel data) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| ContinuousDataAlignmentModel(AlignmentDataModelStats data) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| ContinuousDataAlignmentModel(AlignmentDataModelStats data, int EF, int minSpliceSupport) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| ContinuousDataAlignmentModel(AlignmentDataModelStats data, File[] maskFiles, int minSpliceSupport) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| ContinuousDataAlignmentModel(AlignmentDataModelStats data, File[] maskFiles, int EF, int minSpliceSupport, AlignmentDataModelStats pairedData, AlignmentDataModelStats strandSpecificReads) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| ContinuousDataAlignmentModel(AlignmentDataModelStats data, File[] maskFiles, int EF, int minSpliceSupport, AlignmentDataModelStats pairedData, AlignmentDataModelStats strandSpecificReads, boolean upweight) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| ContinuousDataAlignmentModel(AlignmentDataModelStats data, Map< String, Integer > maskFileData, int EF, int minSpliceSupport, AlignmentDataModelStats pairedData, AlignmentDataModelStats strandSpecificReads) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| ContinuousDataAlignmentModel(AlignmentDataModelStats data, Map< String, Integer > maskFileData, int EF, int minSpliceSupport, AlignmentDataModelStats pairedData, AlignmentDataModelStats strandSpecificReads, boolean upWeight) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| ContinuousDataAlignmentModel(AlignmentDataModelStats data, Map< String, Integer > maskFileData, int EF, int minSpliceSupport, AlignmentDataModelStats pairedData, AlignmentDataModelStats strandSpecificReads, int chunkSize, boolean upWeightSplices) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| ContinuousDataAlignmentModel(AlignmentDataModelStats data, File[] maskFiles, int EF, int minSpliceSupport, AlignmentDataModelStats pairedData) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| ContinuousDataAlignmentModel(AlignmentDataModelStats data, File[] maskFiles, int EF, int minSpliceSupport) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| count(Annotation align) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| CV(Gene gene, IntervalTree< Alignment > tree) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| DEFAULT_INS_SIZE_PVAL | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | static |
| DEFAULT_INSERT_SIZE_FUDGE | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | static |
| DEFAULT_MAKE_GENE_OVERLAP | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | static |
| DEFAULT_MIN_MAPPING_QUALITY | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | static |
| filterGenesByExpression(Map< Gene, List< Double >> countsMap) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| filterPaths(Map< Path, double[]> scores, double alpha2) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | static |
| getAlignmentDataModelStats() | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getBasesCovered(Annotation region) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getBasesCovered(Annotation region, int EF) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getChromosomeLength(String chr) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getChromosomeLengths() | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getCount(Collection< Annotation > Annotation) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getCounts(Map< String, IntervalTree< Annotation >> geneTree, Collection< String > multimappers) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getCountsPerBp(Annotation align, IntervalTree< Alignment > tree) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getCountsPerBp(Gene gene, IntervalTree< Alignment > tree) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getData() | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getDataForAlignment(Annotation align) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getDataForGene(Gene gene) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getDataForGene(Collection< Gene > Annotation) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getGeneCounts(Collection< Gene > genes) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getGeneCountsWithoutDatasetTotals(Collection< Gene > genes) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getGeneExpression(Collection< Gene > genes) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getLambda(String chr) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getNumberMarkers(String chr) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getNumberOfBPs() | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getNumberOfReads(String chr) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getPairedData() | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getPeak(Gene gene, Gene startCodon, IntervalTree< Alignment > tree) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getPeak(Gene gene, Gene startCodon) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getSum(String chr) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| getWidths(String str) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | static |
| hasDataForChromosome(String chr) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| main(String[] args) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | static |
| parseMaskFiles(File[] files) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | static |
| permuteRegions(Annotation align) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| rawRegions(Annotation align) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| resetTreeCache() | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scan(int[] windowSizes, double alpha) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scan(int[] windowSizes, double alpha, String chr) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scanGenome(ContinuousDataAlignmentModel data2, int windowSize, String chr, FileWriter writer, boolean filterSignificance) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scanPRate(Gene gene) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scanPRate(Gene gene, IntervalTree< Alignment > tree) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scanPRate(Gene gene, IntervalTree< Alignment > tree, double localLambda) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scanPRate(Gene gene, IntervalTree< Alignment > tree, double localLambda, int numMarkers) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scanRegion(int fixedWidth, LightweightGenomicAnnotation region) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreGene(Gene align) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreGene(Gene align, double localLambda) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreGene(Gene align, IntervalTree< Alignment > tree, double localLambda) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreGene(Gene align, IntervalTree< Alignment > tree, double localLambda, int numMarkers) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreGene(Gene align, IntervalTree< Alignment > tree) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreGenes(Collection< Gene > set, String chrToUse, IntervalTree< Alignment > tree) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreGenes(Collection< Gene > genes) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreGenes(Collection< Gene > set, String chrToUse) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreGenes(Collection< Gene > set, String chrToUse, int size) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreGenes(BEDFileParser genes) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scorePaths(Collection< Path > paths, double lambda) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scorePaths(Collection< Path > paths, ChromosomeWithBubblesJGraphT graph, double alpha) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | static |
| scorePaths(Collection< Path > paths, double lambda, double numMarkers, double numReads, double RPKMContant, Map< Annotation, Double > localRates, double alpha) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | static |
| scorePathsForOnlyRPKM(Collection< Path > paths) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreSegment(Annotation align) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreSegments(Collection< Annotation > set) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreSegments(Collection< Annotation > set, String chrToUse) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| scoreSegments(Collection< Annotation > set, String chrToUse, boolean ignoreAlpha) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| setAlpha(double alpha) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| setExtensionFactor(int extensionFactor) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| setFindMaxContiguous(boolean findMaxContiguous) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| setMaskFileData(Map< String, Integer > maskedRegionMap) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| setMinContguousSegmentSize(int minSize) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| setMinimumMappingQuality(double minMapQual) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| setMinNumberOfSplices(int minSpliceSupport) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| setTrimEnds(boolean trimEnds) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| setTrimQuantile(double quantile) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| setUpWeightSplices(boolean setFlag) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| trimGeneEnds(Gene gene, double quantile) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| trimMaxContiguous(Gene region, double quantile) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| writeConnections(String save, ChromosomeWithBubblesJGraphT graph) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | |
| writeFullBED(String save, Map< Gene, double[]> map, double alpha) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | static |
| writeFullBED(String save, Collection< Gene > segments) | broad.pda.seq.segmentation.ContinuousDataAlignmentModel | static |
1.8.7
