| addFilter(Predicate< Alignment > filter) | umms.core.model.JCSAlignmentModel | |
| addFilters(Collection< Predicate< Alignment >> filters) | umms.core.model.JCSAlignmentModel | |
| computeGlobalStats() | umms.core.model.JCSAlignmentModel | |
| containsReference(String refName) | umms.core.model.JCSAlignmentModel | |
| coordinateSpace | umms.core.model.JCSAlignmentModel | protected |
| getAlignmentType() | umms.core.model.JCSAlignmentModel | |
| getAverageCountPerPosition(Gene gene) | umms.core.model.JCSAlignmentModel | |
| getAverageCountPerPositionWithThreshold(Gene gene, int minCount) | umms.core.model.JCSAlignmentModel | |
| getBamFile() | umms.core.model.JCSAlignmentModel | |
| getBasesCovered(Annotation region, boolean fullyContained) | umms.core.model.JCSAlignmentModel | |
| getBasesCovered(Annotation region) | umms.core.model.JCSAlignmentModel | |
| getCoordinateSpace() | umms.core.model.JCSAlignmentModel | |
| getCount(Annotation window, boolean fullyContained) | umms.core.model.JCSAlignmentModel | |
| getCount() | umms.core.model.JCSAlignmentModel | |
| getCount(CloseableIterator< AlignmentCount > iter) | umms.core.model.JCSAlignmentModel | |
| getCount(Annotation window) | umms.core.model.JCSAlignmentModel | |
| getCountExcludingRegion(Annotation region, Annotation excluded) | umms.core.model.JCSAlignmentModel | |
| getCountsPerPosition(Gene gene) | umms.core.model.JCSAlignmentModel | |
| getCountsStrandedPerPosition(Annotation gene) | umms.core.model.JCSAlignmentModel | |
| getCountStrandedExcludingRegion(Annotation region, Annotation excluded) | umms.core.model.JCSAlignmentModel | |
| getGlobalCount() | umms.core.model.JCSAlignmentModel | |
| getGlobalCountReferenceSeqs() | umms.core.model.JCSAlignmentModel | |
| getGlobalLambda() | umms.core.model.JCSAlignmentModel | |
| getGlobalLength() | umms.core.model.JCSAlignmentModel | |
| getGlobalNumReads() | umms.core.model.JCSAlignmentModel | |
| getGlobalNumReadsReferenceSeqs() | umms.core.model.JCSAlignmentModel | |
| getGlobalPairedFragments() | umms.core.model.JCSAlignmentModel | |
| getHeader() | umms.core.model.JCSAlignmentModel | |
| getIntronCounts(Annotation intron) | umms.core.model.JCSAlignmentModel | |
| getMedianReadSize(Annotation region, CoordinateSpace coord, int maxSize, int numBins, boolean fullyContained) | umms.core.model.JCSAlignmentModel | |
| getMedianReadSize(Annotation region, CoordinateSpace coord, int maxSize, int numBins) | umms.core.model.JCSAlignmentModel | |
| getOverlappingAnnotations(Annotation region, boolean fullyContained) | umms.core.model.JCSAlignmentModel | |
| getOverlappingReadCounts(Annotation region, boolean fullyContained) | umms.core.model.JCSAlignmentModel | |
| getOverlappingReadReplicateCounts(Annotation region, boolean fullyContained) | umms.core.model.JCSAlignmentModel | |
| getOverlappingReads(String chr) | umms.core.model.JCSAlignmentModel | |
| getOverlappingReads(Annotation region, boolean fullyContained) | umms.core.model.JCSAlignmentModel | |
| getOverlappingSplicedReads(Annotation region, boolean fullyContained) | umms.core.model.JCSAlignmentModel | |
| getOverlappingSplicedReads(String chr) | umms.core.model.JCSAlignmentModel | |
| getPeak(Annotation parent, Annotation region, boolean fullyContained) | umms.core.model.JCSAlignmentModel | |
| getPermutedAnnotations(Annotation region) | umms.core.model.JCSAlignmentModel | |
| getReadIterator() | umms.core.model.JCSAlignmentModel | |
| getReadIterator(Annotation region) | umms.core.model.JCSAlignmentModel | |
| getReadSizeDistribution(CoordinateSpace coord, int maxSize, int numBins) | umms.core.model.JCSAlignmentModel | |
| getReadSizeDistribution(Annotation region, CoordinateSpace coord, int maxSize, int numBins) | umms.core.model.JCSAlignmentModel | |
| getReadSizeDistribution(Annotation region, CoordinateSpace coord, int maxSize, int numBins, boolean fullyContained) | umms.core.model.JCSAlignmentModel | |
| getRefSequenceCounts(String refName) | umms.core.model.JCSAlignmentModel | |
| getRefSequenceLambda(String refName) | umms.core.model.JCSAlignmentModel | |
| getRefSequenceLength(String refName) | umms.core.model.JCSAlignmentModel | |
| getRefSequenceLengths() | umms.core.model.JCSAlignmentModel | |
| getSplicedCount(Alignments alignments, boolean fullyContained) | umms.core.model.JCSAlignmentModel | |
| isValid(Alignment read) | umms.core.model.JCSAlignmentModel | |
| iterator() | umms.core.model.JCSAlignmentModel | |
| JCSAlignmentModel(String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters, boolean readOrCreatePairedEndBam) | umms.core.model.JCSAlignmentModel | |
| JCSAlignmentModel() | umms.core.model.JCSAlignmentModel | |
| JCSAlignmentModel(String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters, boolean readOrCreatePairedEndBam, TranscriptionRead transcriptionRead) | umms.core.model.JCSAlignmentModel | |
| JCSAlignmentModel(String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters, boolean readOrCreatePairedEndBam, TranscriptionRead transcriptionRead, boolean fragment) | umms.core.model.JCSAlignmentModel | |
| JCSAlignmentModel(String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters, boolean readOrCreatePairedEndBam, TranscriptionRead transcriptionRead, String maskedRegionFile) | umms.core.model.JCSAlignmentModel | |
| JCSAlignmentModel(String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters, boolean readOrCreatePairedEndBam, TranscriptionRead transcriptionRead, boolean fragment, String maskedRegionFile) | umms.core.model.JCSAlignmentModel | |
| JCSAlignmentModel(String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters) | umms.core.model.JCSAlignmentModel | |
| JCSAlignmentModel(String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters, TranscriptionRead transcriptionRead) | umms.core.model.JCSAlignmentModel | |
| JCSAlignmentModel(String bamFile, CoordinateSpace coordinateSpace, boolean readOrCreatePairedEndBam) | umms.core.model.JCSAlignmentModel | |
| JCSAlignmentModel(String bamFile, CoordinateSpace coordinateSpace, boolean readOrCreatePairedEndBam, TranscriptionRead transcriptionRead) | umms.core.model.JCSAlignmentModel | |
| JCSAlignmentModel(String bamFile, CoordinateSpace coordinateSpace) | umms.core.model.JCSAlignmentModel | |
| JCSAlignmentModel(String bamFile, CoordinateSpace coordinateSpace, TranscriptionRead transcriptionRead) | umms.core.model.JCSAlignmentModel | |
| main(String[] args) | umms.core.model.JCSAlignmentModel | static |
| removeFilter(Predicate< Alignment > readFilter) | umms.core.model.JCSAlignmentModel | |
| scan(Annotation region, int windowSize, int overlap) | umms.core.model.JCSAlignmentModel | |
| size() | umms.core.model.JCSAlignmentModel | |
| windowIterator(int windowSize, int overlap) | umms.core.model.JCSAlignmentModel | |
1.8.7
