Static Public Member Functions
static Set< Annotation >	collapseByIntersection (Collection<?extends Annotation > alignments, boolean intersection)

static Collection< Annotation >	DecollapseByIntronLocation (Collection< Annotation > exons, Collection< Annotation > introns, String strand)

static Collection< Annotation >	filter (Collection< Annotation > introns, String strand)

static Collection< Annotation >	DecollapseByIntronLocation (Collection< Annotation > exons, Collection< Annotation > introns)

static Collection< Annotation >	DecollapseByIntronLocationOld (Collection< Annotation > exons, Collection< Annotation > introns)

static Collection< Annotation >	DecollapseByIntronLocationWorking (Collection< Annotation > exons, Collection< Annotation > introns)

static Collection< Gene >	updateBoundariesWithoutCrossingIntrons (Collection< Gene > genes)

static Map< String, IntervalTree< Annotation > >	makeIntervalTree (Collection<?extends Annotation > alignments)

static Map< String, IntervalTree< Gene > >	makeIntervalTreeForGenes (Collection< Gene > alignments)

static Collection< Annotation >	CollapseGenesByIntersection (Collection< Gene > temp, boolean intersection)

static Map< String, IntervalTree< Annotation > >	makeIntervalTreeForGeneExons (Collection< Gene > genes)

Member Function Documentation

static Set<Annotation> broad.core.util.CollapseByIntersection.collapseByIntersection	(	Collection<?extends Annotation >	alignments,
		boolean	intersection
	)

static

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static Collection<Annotation> broad.core.util.CollapseByIntersection.CollapseGenesByIntersection	(	Collection< Gene >	temp,
		boolean	intersection
	)

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static Collection<Annotation> broad.core.util.CollapseByIntersection.DecollapseByIntronLocation	(	Collection< Annotation >	exons,
		Collection< Annotation >	introns,
		String	strand
	)

static

This method returns only exons that are trimmed down by intron location. If its fully within intron it just returns it. If bases overlap intron it trims down

Parameters

exons
introns
strand

Returns

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static Collection<Annotation> broad.core.util.CollapseByIntersection.DecollapseByIntronLocation	(	Collection< Annotation >	exons,
		Collection< Annotation >	introns
	)

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static Collection<Annotation> broad.core.util.CollapseByIntersection.DecollapseByIntronLocationOld	(	Collection< Annotation >	exons,
		Collection< Annotation >	introns
	)

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static Collection<Annotation> broad.core.util.CollapseByIntersection.DecollapseByIntronLocationWorking	(	Collection< Annotation >	exons,
		Collection< Annotation >	introns
	)

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static Collection<Annotation> broad.core.util.CollapseByIntersection.filter	(	Collection< Annotation >	introns,
		String	strand
	)

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static Map<String, IntervalTree<Annotation> > broad.core.util.CollapseByIntersection.makeIntervalTree ( Collection<?extends Annotation > alignments )

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