| Chromosome(final String name) | broad.pda.feature.genome.Chromosome | |
| Chromosome(String name, String agpFile) | broad.pda.feature.genome.Chromosome | |
| compareNames(String name1, String name2) | broad.pda.feature.genome.Chromosome | static |
| compareTo(Object o) | broad.pda.feature.genome.Chromosome | |
| delete(SequenceRegion region) | broad.pda.feature.genome.Chromosome | |
| drawRandomRegion(int size) | broad.pda.feature.genome.Chromosome | |
| extractRegion(SequenceRegion region) | broad.pda.feature.genome.Chromosome | |
| extractRegions(List<?extends SequenceRegion > regions) | broad.pda.feature.genome.Chromosome | |
| gaps() | broad.pda.feature.genome.Chromosome | |
| getChromosomeNumber() | broad.pda.feature.genome.Chromosome | |
| getChromosomeNumber(String name) | broad.pda.feature.genome.Chromosome | static |
| getName() | broad.pda.feature.genome.Chromosome | |
| getRegion(SequenceRegion region) | broad.pda.feature.genome.Chromosome | |
| getRegion(SequenceRegion region, boolean softmask) | broad.pda.feature.genome.Chromosome | |
| getRegion(SequenceRegion region, boolean softmask, Map< String, IntervalTree< Alignments >> okRepeats) | broad.pda.feature.genome.Chromosome | |
| getRegions(List<?extends GenomicAnnotation > annotations, int padding) | broad.pda.feature.genome.Chromosome | |
| getSequence() | broad.pda.feature.genome.Chromosome | |
| getShortArm() | broad.pda.feature.genome.Chromosome | |
| getSymbol() | broad.pda.feature.genome.Chromosome | |
| getUngappedSize() | broad.pda.feature.genome.Chromosome | |
| insert(SequenceRegion region, LightweightGenomicAnnotation insertPoint) | broad.pda.feature.genome.Chromosome | |
| invert(SequenceRegion region) | broad.pda.feature.genome.Chromosome | |
| isAutosome() | broad.pda.feature.genome.Chromosome | |
| isAutosome(String name) | broad.pda.feature.genome.Chromosome | static |
| isSexChromosome() | broad.pda.feature.genome.Chromosome | |
| isSexChromosome(String name) | broad.pda.feature.genome.Chromosome | static |
| length() | broad.pda.feature.genome.Chromosome | |
| loadSequence() | broad.pda.feature.genome.Chromosome | |
| setSequenceFile(File file) | broad.pda.feature.genome.Chromosome | |
| shuffle(GenomicAnnotation toShuffle, List<?extends GenomicAnnotation > toAvoid) | broad.pda.feature.genome.Chromosome | |
| shuffle(List<?extends GenomicAnnotation > toShuffle, List<?extends GenomicAnnotation > toAvoid) | broad.pda.feature.genome.Chromosome | |
| shuffleWithinValid(Annotation toShuffle, List<?extends Annotation > valid) | broad.pda.feature.genome.Chromosome | |
| shuffleWithinValid(List<?extends Annotation > toShuffle, List<?extends Annotation > valid) | broad.pda.feature.genome.Chromosome | |
| unloadSequence() | broad.pda.feature.genome.Chromosome | |
1.8.7
