| addBlock(String name, int start, int end) | broad.core.sequence.SequenceRegion | |
| addExtraScore(double score) | broad.core.sequence.SequenceRegion | |
| almostEqual(LightweightGenomicAnnotation other, int fudge) | broad.core.sequence.SequenceRegion | |
| append(String partialSequence) | broad.core.sequence.Sequence | |
| append(char c) | broad.core.sequence.Sequence | |
| buildKmerMap(int kmer) | broad.core.sequence.Sequence | |
| chunk(int chunkSize, int chunkOverlap) | broad.core.sequence.Sequence | |
| compareTo(GenomicAnnotation arg0) | broad.core.sequence.SequenceRegion | |
| compareTo(LightweightGenomicAnnotation b) | broad.core.sequence.SequenceRegion | |
| compareTo(Annotation arg0) | broad.core.sequence.SequenceRegion | |
| compareToAnnotation(Annotation b) | broad.core.sequence.SequenceRegion | |
| complement() | broad.core.sequence.SequenceRegion | |
| broad::core::sequence::Sequence.complement(String seq) | broad.core.sequence.Sequence | static |
| compute454Flow(char[] flowOrder) | broad.core.sequence.Sequence | |
| compute454Flow(char[] flowOrder, int start, int end) | broad.core.sequence.Sequence | |
| computeGCContent(String dnaString) | broad.core.sequence.Sequence | static |
| computeSequenceComposition(String dnaString) | broad.core.sequence.Sequence | static |
| contains(LightweightGenomicAnnotation other) | broad.core.sequence.SequenceRegion | |
| contains(Annotation other) | broad.core.sequence.SequenceRegion | |
| broad::core::sequence::Sequence.contains(String motif) | broad.core.sequence.Sequence | |
| copy() | broad.core.sequence.SequenceRegion | |
| countSoftMaskedBases() | broad.core.sequence.Sequence | |
| decode(short[] shortEncodedSequence) | broad.core.sequence.Sequence | static |
| disect(Annotation a) | broad.core.sequence.SequenceRegion | |
| disect(List<?extends Annotation > disectors) | broad.core.sequence.SequenceRegion | |
| encodeSequence() | broad.core.sequence.Sequence | |
| encodeSequence(StringBuilder bases) | broad.core.sequence.Sequence | static |
| encodeSequenceAsVector() | broad.core.sequence.Sequence | |
| encodeSequenceIgnoreCase() | broad.core.sequence.Sequence | |
| encodeSequenceIgnoreCase(boolean distinguishMissingSequence) | broad.core.sequence.Sequence | |
| encodeSequenceIgnoreCase(StringBuilder sequence) | broad.core.sequence.Sequence | static |
| encodeSequenceIgnoreCase(StringBuilder sequence, boolean distinguishMissingSequence) | broad.core.sequence.Sequence | static |
| equals(Annotation other) | broad.core.sequence.SequenceRegion | |
| equals(Annotation other, boolean useOrientation) | broad.core.sequence.SequenceRegion | |
| expand(int deltaStart, int deltaEnd) | broad.core.sequence.SequenceRegion | |
| extractRegionBasedOnGC(float targetGC, int size, int buffer) | broad.core.sequence.SequenceRegion | |
| findUngappedSequenceChunks() | broad.core.sequence.Sequence | |
| fullyContains(Annotation annotation) | broad.core.sequence.SequenceRegion | |
| gcContent() | broad.core.sequence.Sequence | |
| generateAll5Mers() | broad.core.sequence.Sequence | static |
| generateAllKmers(int k) | broad.core.sequence.Sequence | static |
| generateRandomSequence(int oligoSize) | broad.core.sequence.Sequence | static |
| get3Prime(String seq, int numBases) | broad.core.sequence.Sequence | static |
| getAbsoluteEnd(int absoluteStart) | broad.core.sequence.SequenceRegion | |
| getAbsoluteStart(int absoluteStart) | broad.core.sequence.SequenceRegion | |
| getAntisense() | broad.core.sequence.Sequence | |
| getBlocks() | broad.core.sequence.SequenceRegion | |
| getBlocks(boolean oriented) | broad.core.sequence.SequenceRegion | |
| getChr() | broad.core.sequence.SequenceRegion | |
| getChromosome() | broad.core.sequence.SequenceRegion | |
| getChromosomeString() | broad.core.sequence.SequenceRegion | |
| getContainingSequenceId() | broad.core.sequence.SequenceRegion | |
| getDistanceTo(LightweightGenomicAnnotation other) | broad.core.sequence.SequenceRegion | |
| getDistanceTo(Annotation other) | broad.core.sequence.SequenceRegion | |
| getEncodedSequence() | broad.core.sequence.Sequence | |
| getEnd() | broad.core.sequence.SequenceRegion | |
| getExtraScore(int i) | broad.core.sequence.SequenceRegion | |
| getExtraScores() | broad.core.sequence.SequenceRegion | |
| getFivePrimeBases() | broad.core.sequence.SequenceRegion | |
| getFullInfoString() | broad.core.sequence.SequenceRegion | |
| getGapsSize() | broad.core.sequence.Sequence | |
| getId() | broad.core.sequence.SequenceRegion | |
| getLength() | broad.core.sequence.SequenceRegion | |
| getLengthOnReference() | broad.core.sequence.SequenceRegion | |
| getLocationString() | broad.core.sequence.SequenceRegion | |
| getMatches(String s, int windowStart, int windowEnd, boolean includeRC) | broad.core.sequence.Sequence | |
| getMiddle() | broad.core.sequence.SequenceRegion | |
| getMidpoint() | broad.core.sequence.SequenceRegion | |
| getName() | broad.core.sequence.SequenceRegion | |
| getOrientation() | broad.core.sequence.SequenceRegion | |
| getOrientedEnd() | broad.core.sequence.SequenceRegion | |
| getOrientedStart() | broad.core.sequence.SequenceRegion | |
| getOverlap(LightweightGenomicAnnotation other) | broad.core.sequence.SequenceRegion | |
| getOverlap(Annotation other) | broad.core.sequence.SequenceRegion | |
| getPositionAtReferenceCoordinate(int referenceCoordinate) | broad.core.sequence.SequenceRegion | |
| getPositionAtReferenceCoordinate(int referenceCoordinate, boolean ignoreOrientation) | broad.core.sequence.SequenceRegion | |
| getReferenceCoordinateAtPosition(int positionInAnnotation) | broad.core.sequence.SequenceRegion | |
| getReferenceCoordinateAtPosition(int positionInAnnotation, boolean ignoreOrientation) | broad.core.sequence.SequenceRegion | |
| getReferenceName() | broad.core.sequence.SequenceRegion | |
| getRefseqGeneName() | broad.core.sequence.Sequence | |
| getRefseqRnaClassName() | broad.core.sequence.Sequence | |
| getRefseqSpeciesName() | broad.core.sequence.Sequence | |
| getRegion(int start, int end) | broad.core.sequence.SequenceRegion | |
| broad::core::sequence::Sequence.getRegion(SequenceRegion region) | broad.core.sequence.Sequence | |
| broad::core::sequence::Sequence.getRegion(SequenceRegion region, boolean softmask) | broad.core.sequence.Sequence | |
| broad::core::sequence::Sequence.getRegion(SequenceRegion region, boolean softmask, Map< String, IntervalTree< Alignments >> okRepeats) | broad.core.sequence.Sequence | |
| getRegionEnd() | broad.core.sequence.SequenceRegion | |
| getRegions(List<?extends SequenceRegion > regions) | broad.core.sequence.Sequence | |
| getRegionStart() | broad.core.sequence.SequenceRegion | |
| getSAMEnd() | broad.core.sequence.SequenceRegion | |
| getSAMStart() | broad.core.sequence.SequenceRegion | |
| getScore() | broad.core.sequence.SequenceRegion | |
| getSequence() | broad.core.sequence.SequenceRegion | |
| getSequenceBases() | broad.core.sequence.Sequence | |
| getSequenceBuilder() | broad.core.sequence.Sequence | |
| getSize() | broad.core.sequence.SequenceRegion | |
| getSlider(int windowSize, int overlap) | broad.core.sequence.SequenceRegion | |
| getSoftmaskedRegions() | broad.core.sequence.Sequence | |
| getSpliceConnections() | broad.core.sequence.SequenceRegion | |
| getStart() | broad.core.sequence.SequenceRegion | |
| getStrand() | broad.core.sequence.SequenceRegion | |
| getSubSequence(SequenceRegion region, int extension) | broad.core.sequence.Sequence | |
| getSubSequence(String name, int start, int end, int extension) | broad.core.sequence.Sequence | |
| getSubSequence(String name, int start, int end) | broad.core.sequence.Sequence | |
| getSubsequence(Gene annot) | broad.core.sequence.Sequence | |
| getSubsequence(Annotation annot) | broad.core.sequence.Sequence | |
| getThreePrimeBases() | broad.core.sequence.SequenceRegion | |
| getVectorEncodedSequence() | broad.core.sequence.Sequence | |
| hasOrientation() | broad.core.sequence.SequenceRegion | |
| INF | broad.core.sequence.SequenceRegion | static |
| inReversedOrientation() | broad.core.sequence.SequenceRegion | |
| intersect(LightweightGenomicAnnotation other) | broad.core.sequence.SequenceRegion | |
| intersect(List<?extends Annotation > annotations) | broad.core.sequence.SequenceRegion | |
| intersect(Annotation other) | broad.core.sequence.SequenceRegion | |
| isFlankedBy(TwoSubjectAnnotation twoSubjectAnnotation, int buffer) | broad.core.sequence.SequenceRegion | |
| isForwardStrand() | broad.core.sequence.Sequence | |
| isGap(int position) | broad.core.sequence.Sequence | |
| isNegativeStrand() | broad.core.sequence.SequenceRegion | |
| isUnoriented() | broad.core.sequence.SequenceRegion | |
| length() | broad.core.sequence.SequenceRegion | |
| LONG_READ_FLOW | broad.core.sequence.Sequence | static |
| mask(Annotation region, boolean softmask) | broad.core.sequence.Sequence | |
| maskSoftmaskedRegions() | broad.core.sequence.Sequence | |
| mayHaveBlocks() | broad.core.sequence.SequenceRegion | |
| minus(Annotation other) | broad.core.sequence.SequenceRegion | |
| minus(List<?extends Annotation > others) | broad.core.sequence.SequenceRegion | |
| minus(Collection<?extends Annotation > others) | broad.core.sequence.SequenceRegion | |
| moveToCoordinate(int i) | broad.core.sequence.SequenceRegion | |
| numBlocks() | broad.core.sequence.SequenceRegion | |
| overlaps(LightweightGenomicAnnotation other, int buffer) | broad.core.sequence.SequenceRegion | |
| overlaps(LightweightGenomicAnnotation other) | broad.core.sequence.SequenceRegion | |
| overlaps(Collection<?extends Annotation > others, int buffer) | broad.core.sequence.SequenceRegion | |
| overlaps(Collection<?extends Annotation > others) | broad.core.sequence.SequenceRegion | |
| overlaps(Annotation other, int buffer) | broad.core.sequence.SequenceRegion | |
| overlaps(Annotation other) | broad.core.sequence.SequenceRegion | |
| overlaps(Annotation other, int buffer, boolean considerStrand) | broad.core.sequence.SequenceRegion | |
| overlaps(Annotation other, boolean considerOrientation) | broad.core.sequence.SequenceRegion | |
| overlapsStranded(Annotation other) | broad.core.sequence.SequenceRegion | |
| percentGC() | broad.core.sequence.SequenceRegion | |
| removeExtraScores() | broad.core.sequence.SequenceRegion | |
| reverse() | broad.core.sequence.Sequence | |
| reverseSequence(Sequence seq) | broad.core.sequence.Sequence | static |
| reverseSequence(String seq) | broad.core.sequence.Sequence | static |
| scramble() | broad.core.sequence.Sequence | |
| Sequence(String id) | broad.core.sequence.Sequence | |
| Sequence(String id, boolean isLarge) | broad.core.sequence.Sequence | |
| Sequence(String id, int expectedSize) | broad.core.sequence.Sequence | |
| SequenceRegion(String containingSequenceId) | broad.core.sequence.SequenceRegion | |
| SequenceRegion(String containingSequenceId, String chr, int start, int end) | broad.core.sequence.SequenceRegion | |
| SequenceRegion(String containingSequenceId, Annotation annotation) | broad.core.sequence.SequenceRegion | |
| setCapacity(int size) | broad.core.sequence.Sequence | |
| setCharAt(int position, char newCharacter) | broad.core.sequence.Sequence | |
| setChromosome(String chr) | broad.core.sequence.SequenceRegion | |
| setEnd(int end) | broad.core.sequence.SequenceRegion | |
| setForwardStrand(boolean isForwardStrand) | broad.core.sequence.Sequence | |
| setId(String id) | broad.core.sequence.SequenceRegion | |
| setName(String name) | broad.core.sequence.SequenceRegion | |
| setOrientation(String orientation) | broad.core.sequence.SequenceRegion | |
| setOrientation(char orientation) | broad.core.sequence.SequenceRegion | |
| setOrientation(Strand orientation) | broad.core.sequence.SequenceRegion | |
| setOrientedEnd(int orientedEnd) | broad.core.sequence.SequenceRegion | |
| setOrientedStart(int orientedStart) | broad.core.sequence.SequenceRegion | |
| setReferenceName(String refName) | broad.core.sequence.SequenceRegion | |
| setRegionEnd(int regionEnd) | broad.core.sequence.SequenceRegion | |
| setRegionStart(int regionStart) | broad.core.sequence.SequenceRegion | |
| setReversedOrientation(boolean reversed) | broad.core.sequence.SequenceRegion | |
| setScore(double score) | broad.core.sequence.SequenceRegion | |
| setSequence(Sequence seq) | broad.core.sequence.SequenceRegion | |
| setSequenceBases(String sequence) | broad.core.sequence.Sequence | |
| setStart(int start) | broad.core.sequence.SequenceRegion | |
| shift(int delta) | broad.core.sequence.SequenceRegion | |
| SHORT_ENCODED_a | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_A | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_C | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_c | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_g | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_G | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_GAP | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_N | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_T | broad.core.sequence.Sequence | static |
| SHORT_ENCODED_t | broad.core.sequence.Sequence | static |
| SHORT_READ_FLOW | broad.core.sequence.Sequence | static |
| shuffle() | broad.core.sequence.Sequence | |
| size() | broad.core.sequence.SequenceRegion | |
| stitchTo(LightweightGenomicAnnotation other) | broad.core.sequence.SequenceRegion | |
| stitchTo(Annotation next) | broad.core.sequence.SequenceRegion | |
| takeIntersection(LightweightGenomicAnnotation other) | broad.core.sequence.SequenceRegion | |
| takeUnion(LightweightGenomicAnnotation other) | broad.core.sequence.SequenceRegion | |
| toBED() | broad.core.sequence.SequenceRegion | |
| toBED(int r, int g, int b) | broad.core.sequence.SequenceRegion | |
| toBEDGraph() | broad.core.sequence.SequenceRegion | |
| toCigar() | broad.core.sequence.SequenceRegion | |
| toShortBED() | broad.core.sequence.SequenceRegion | |
| toString() | broad.core.sequence.SequenceRegion | |
| toUCSC() | broad.core.sequence.SequenceRegion | |
| trim(int deltaStart, int deltaEnd) | broad.core.sequence.SequenceRegion | |
| union(Annotation other) | broad.core.sequence.SequenceRegion | |
| unloadAllSequences() | broad.core.sequence.Sequence | |
| unloadEncodedSequence() | broad.core.sequence.Sequence | |
| unloadSequence() | broad.core.sequence.Sequence | |
| uppercase() | broad.core.sequence.Sequence | |
1.8.7
