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broad.pda.gene.GeneTools Member List

This is the complete list of members for broad.pda.gene.GeneTools, including all inherited members.

intersectGeneSets(Collection< Gene > set1, Collection< Gene > set2, boolean takeComplement)broad.pda.gene.GeneToolsstatic
main(String[] args)broad.pda.gene.GeneToolsstatic
merge(Map< String, Collection< Gene >> originalMap)broad.pda.gene.GeneToolsstatic
merge(Collection< Gene > original)broad.pda.gene.GeneToolsstatic
mergeByGtfGeneId(String inFile, String outFile, String outFormat, String src, boolean writeMode)broad.pda.gene.GeneToolsstatic
mergeSets(Map< String, IntervalTree< Gene >> set1, Map< String, IntervalTree< Gene >> set2)broad.pda.gene.GeneToolsstatic
orientationForGene(Gene g, Sequence cSeq)broad.pda.gene.GeneToolsstatic
orientationFromSpliceSites(Annotation introns, Sequence seq, boolean onlyCanonical)broad.pda.gene.GeneToolsstatic
orientationFromSpliceSites(Annotation introns, Sequence chrSeq)broad.pda.gene.GeneToolsstatic
overlap(Map< String, IntervalTree< Gene >> set1, Map< String, IntervalTree< Gene >>set2, Boolean byExon)broad.pda.gene.GeneToolsstatic
selectHighScoringIsoform(Gene transcript, BEDFileParser set)broad.pda.gene.GeneToolsstatic
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