| clearFullIntervalTreeAsAlignmentsCached(String chr) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| countReads(Alignment record) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| GenericAlignmentDataModel(String filename, String lengthFile, boolean upweightSplices, double minMappingQuality, boolean removeDuplicatesFlag, boolean weighReadCounts, String strand, boolean loadPairsAsFragments) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| GenericAlignmentDataModel(String filename, String lengthFile, boolean upweightSplices, double minMappingQuality) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| GenericAlignmentDataModel(String filename, String lengthFile) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| GenericAlignmentDataModel(String filename, String lengthFile, int minMappingQuality) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| GenericAlignmentDataModel(String filename, String lengthFile, boolean upweightSplices) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| GenericAlignmentDataModel(String filename, String lengthFile, boolean upweightSplices, int minMappingQuality, boolean removeDuplicatesFlag) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| GenericAlignmentDataModel(String filename, String lengthFile, int minMappingQuality, boolean removeDuplicatesFlag) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| GenericAlignmentDataModel(String filename, String lengthFile, boolean removeDuplicatesFlag, boolean weighReadCounts) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| GenericAlignmentDataModel(String filename, String lengthFile, boolean upweightSplices, boolean removeDuplicatesFlag, boolean weighReadCounts) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| GenericAlignmentDataModel(String filename, String lengthFile, boolean upweightSplices, int minMappingQuality, boolean removeDuplicatesFlag, boolean weighReadCounts) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| GenericAlignmentDataModel(String filename, String lengthFile, boolean upweightSplices, int minMappingQuality, boolean removeDuplicatesFlag, boolean weighReadCounts, String strand) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getAnnotationOverlappingRegion(Annotation align) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getBasesCovered(Annotation region, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getBasesCoveredPerAlignment(Gene gene, IntervalTree< Alignment > tree, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getChrLength(String chr) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getChrLengths() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getChromosomeLength(String chr) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getChromosomeLengths() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getChromosomeReadIterator(String chromosome) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getChrReadIterator(String chromosome) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getChunkEnd() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getChunkStart() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCounts(String chr) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsOfUniqueOverlappers(Annotation target, Annotation exclude, IntervalTree< Alignment > tree, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsOfUniqueOverlappers(Annotation target, Gene exclude, IntervalTree< Alignment > tree, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsOnBase(String chr, int index) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsOnWindow(String chr, int startIndex, int endIndex) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsPerAlignment(Annotation align, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsPerAlignment(Annotation align) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsPerAlignment(Annotation align, IntervalTree< Alignment > tree, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsPerAlignment(Gene gene, IntervalTree< Alignment > tree, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsPerAlignment(Annotation[] Annotation, IntervalTree< Alignment > tree, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsPerAlignment(Annotation[] Annotation, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsPerAlignment(Annotation align, Map< String, IntervalTree< Annotation >> goodExonTree, IntervalTree< Alignment > tree, int extensionFactor) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsPerAlignmentForPolyA(Annotation align, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsPerAlignmentFullyContained(Gene gene, IntervalTree< Alignment > tree, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsPerAlignmentUncached(String chr, int startIndex, int endIndex) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsPerAlignmentWithSameEndpointForPolyA(Annotation align, int EF, boolean polyAIsOnRight, int typicalOriginalAlignmentLength, int maxDistanceFromOriginalAlignmentEndpoint) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsPerAnnotationtranded(Gene gene, IntervalTree< Alignment > tree, int EF, String orientation) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsWithinExons(Annotation align, IntervalTree< Alignment > tree, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getCountsWithinExons(Annotation align, Iterator< Alignment > iter, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getExonAnnotationOverlappingRegion(Annotation align) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getExonAnnotationOverlappingRegion(IntervalTree< Alignment > tree) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getFullIntervalTreeAsAnnotation(String chr) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getGeneCounts(Gene gene, int extensionFactor) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getIntervalTree(String chr, int start, int end) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getIntervalTreeCached(String chr, int start, int end) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getIntervalTreeTruncated(String chr, int start, int end) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getIntervalTreeTruncatedCached(String chromosome, int start, int end) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getMinimumMappingQuality() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getModelFilePath() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getNumberOfSplicedReads(Annotation align) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getNumberOfSplicedReads() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getOverlappingRegions(String chr) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getPeak(Gene gene, Gene startCodon, IntervalTree< Alignment > tree, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getReadIterator() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getReadIterator(Annotation region) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getSamHeader() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getScorePerAlignmentFromCache(Gene window, IntervalTree< Alignment > chunkAlignmentTree, int extensionFactor) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getSplicedReadExons(String chr) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getSplicedReads(Annotation align) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getSplicedReads(Annotation align, final int minIntronSize, final int maxIntronSize, int minNumIntrons, Sequence chrSeq) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getSplicedReads(Annotation align, final int minIntronSize, final int maxIntronSize) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getSplicedReads(Annotation region, Predicate< Annotation > filter) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getSplicedReads(Annotation region, Collection< Predicate< Annotation >> filters, int minNumIntrons) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getSplicedReads(Annotation region, Collection< Predicate< Annotation >> filters, int minNumIntrons, Sequence chrSeq) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getSplicedReads(Annotation region, Collection< Predicate< Annotation >> filters) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getSplicedReads(Annotation region, Collection< Predicate< Annotation >> filters, Sequence chrSeq) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getSplicedReads(int minIntronSize, int maxIntronSize) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| broad::pda::seq::segmentation::AlignmentDataModel.getSplicedReads(Annotation align, int minIntronSize, int maxIntronSize) | broad.pda.seq.segmentation.AlignmentDataModel | |
| getSpliceWeightFactor() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getTotalNumberOfMappedReads() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getTotalNumberOfMappedStrandedReads() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getTotalNumberOfReads() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getTotalNumberOfStrandedReads() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| getWeight() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| hasNextExon(String chr) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| isNegativeStranded() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| isPositiveStranded() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| isStranded() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| loadedPairsAsFragments() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| passes(Gene gene, IntervalTree< Alignment > tree, int EF, double cutoff) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| passesCutoff(Annotation align, IntervalTree< Alignment > tree, int EF, double threshold) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| resetTreeCache(String chr) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| resetTreeCache() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| restartIterator() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| setChunkSize(int chunkSize) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| setExtensionFactor(int extensionFactor) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| setFirstRead() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| setMinimumMappingQuality(double minimumMappingQual) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| setNegativeStranded() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| setNormalizationStrategy(ReadCountNormalizer normalizer) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| setPositiveStranded() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| setRemoveDuplicatesFlag(boolean flag) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| setSecondRead() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| setWeighReadCountsFlag(boolean flag) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| unsetStranded() | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
| updateGeneByFirstCounts(Gene gene, IntervalTree< Alignment > tree, int EF) | broad.pda.seq.segmentation.GenericAlignmentDataModel | |
1.8.7
