| AlignmentDataModelStats() | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| AlignmentDataModelStats(AlignmentDataModel data, Map< String, Integer > maskedRegions, String chr) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| AlignmentDataModelStats(AlignmentDataModel data, Map< String, Integer > maskedRegions, String chr, double lambda, boolean loadChromosomeStats) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| AlignmentDataModelStats(AlignmentDataModel data, Map< String, Integer > maskedRegions) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| AlignmentDataModelStats(AlignmentDataModel data, Map< String, Integer > maskedRegions, Map< String, Double > readsPerChromosome) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| AlignmentDataModelStats(AlignmentDataModel data, Map< String, Integer > maskedRegions, String chr, boolean loadChromosomeStats) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| AlignmentDataModelStats(AlignmentDataModel data, Map< String, Integer > maskedRegions, double lambda) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| AlignmentDataModelStats(AlignmentDataModel data, Map< String, Integer > maskedRegions, double lambda, boolean loadChromosomeStats) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| AlignmentDataModelStats(AlignmentDataModel data, Map< String, Integer > maskedRegions, String chr, double lambda) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| AlignmentDataModelStats(AlignmentDataModel data, String chr) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| AlignmentDataModelStats(AlignmentDataModel data) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| chromosomeLength(String chr) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| count(Annotation align, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| countWithinExon(Annotation align, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getAnnotationOverlappingRegion(Annotation Annotation) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getChromosomeLengths() | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getChunkEnd() | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getChunkStart() | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getCounts(Collection< Annotation > Annotation, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getCountsOfUniqueOverlappers(Annotation startPosition, Annotation window, IntervalTree< Alignment > chunkAlignmentTree, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getCountsPerAlignment(Annotation align, IntervalTree< Alignment > tree, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getCountsPerAlignment(Gene window, IntervalTree< Alignment > tree, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getCountsPerAlignment(Annotation align, Map< String, IntervalTree< Annotation >> exonTree, IntervalTree< Alignment > tree, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getData() | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getExonAnnotationOverlappingRegion(Annotation align) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getGeneCounts(Collection< Gene > genes, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getGeneCountsWithoutDatasetTotals(Collection< Gene > genes, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getGeneExpression(Collection< Gene > genes, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getGlobalRPKMConstant() | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getIntervalTree(LightweightGenomicAnnotation region) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getIntervalTree(String chr, int start, int end) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getIntervalTreeCached(String chr, int start, int end) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getIntervalTreeTruncatedCached(String chromosome, int start, int end) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getLambda(String chr) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getMaskedRegionsSize(String chr) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getMinimumMappingQuality() | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getNumberMarkers(String chr) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getNumberOfReads() | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getNumberOfReads(String chr) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getNumberOfReadsByChr(String chr) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getPeak(Gene gene, Gene startCodon, IntervalTree< Alignment > tree, int EF) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getReadIterator() | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getReadIterator(Annotation region) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getRPKMConstant(String chr) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getScorePerAlignmentFromCache(Gene window, IntervalTree< Alignment > chunkAlignmentTree, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getSplicedReads(Annotation chrRegion, int i, int j) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getSplicedReads(Annotation region, List< Predicate< Annotation >> filters, int minNumIntrons) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getSplicedReads(Annotation region, int minIntronSize, int maxIntronSize, int minNumberOfSplices, Sequence chrSequence) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getSpliceWeightFactor() | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getSum(String chr) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| getTotalReads() | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| init(Map< String, Integer > maskedRegions, double lambda, boolean loadChromosomeStats) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| init(Map< String, Integer > maskedRegions, double lambda, boolean loadChromosomeStats, Map< String, Double > readsByChr) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| isPaired() | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| normalizeReadCountsToBaseModel(AlignmentDataModelStats baseline) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| passes(Gene window, IntervalTree< Alignment > chunkAlignmentTree, int i, int critVal) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| resetTreeCache() | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| resetTreeCache(String chr) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| scanPRate(Gene gene, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| scanPRate(LightweightGenomicAnnotation annotation, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| scanPRate(Gene gene, IntervalTree< Alignment > tree, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| scanPRate(Annotation align, IntervalTree< Alignment > tree, double localLambda, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| scanPRate(Annotation align, double readCount, int extenstionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| scanPRate(Annotation align, double readCount, double localLambda, int extenstionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| scanPRate(Gene gene, IntervalTree< Alignment > tree, double localLambda, int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| scanPRate(Gene gene, IntervalTree< Alignment > tree, double localLambda, int extensionFactor, double numMarkers) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| scanRegion(int fixedWidth, LightweightGenomicAnnotation region) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| setAlignmentDataModel(AlignmentDataModel data) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| setChunkSize(int chunkSize) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| setCountNormalizer(ReadCountNormalizer normalizer) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| setExtensionFactor(int extensionFactor) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| setLambda(String chr, double numberOfReads) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| setMinimumMappingQuality(double minMapQual) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| setNumberOfMarkers(String chr, double numMarkers2) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| setNumberOfReads(String chr, double numberOfReads2) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
| setStoredStats(StoredAlignmentStats sas) | broad.pda.seq.segmentation.AlignmentDataModelStats | |
1.8.7
