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broad.core.util.CollapseByIntersection Member List

This is the complete list of members for broad.core.util.CollapseByIntersection, including all inherited members.

collapseByIntersection(Collection<?extends Annotation > alignments, boolean intersection)broad.core.util.CollapseByIntersectionstatic
CollapseGenesByIntersection(Collection< Gene > temp, boolean intersection)broad.core.util.CollapseByIntersectionstatic
DecollapseByIntronLocation(Collection< Annotation > exons, Collection< Annotation > introns, String strand)broad.core.util.CollapseByIntersectionstatic
DecollapseByIntronLocation(Collection< Annotation > exons, Collection< Annotation > introns)broad.core.util.CollapseByIntersectionstatic
DecollapseByIntronLocationOld(Collection< Annotation > exons, Collection< Annotation > introns)broad.core.util.CollapseByIntersectionstatic
DecollapseByIntronLocationWorking(Collection< Annotation > exons, Collection< Annotation > introns)broad.core.util.CollapseByIntersectionstatic
filter(Collection< Annotation > introns, String strand)broad.core.util.CollapseByIntersectionstatic
makeIntervalTree(Collection<?extends Annotation > alignments)broad.core.util.CollapseByIntersectionstatic
makeIntervalTreeForGeneExons(Collection< Gene > genes)broad.core.util.CollapseByIntersectionstatic
makeIntervalTreeForGenes(Collection< Gene > alignments)broad.core.util.CollapseByIntersectionstatic
updateBoundariesWithoutCrossingIntrons(Collection< Gene > genes)broad.core.util.CollapseByIntersectionstatic