umms.core.scripture.BuildScriptureCoordinateSpace Member List

This is the complete list of members for umms.core.scripture.BuildScriptureCoordinateSpace, including all inherited members.

BuildScriptureCoordinateSpace(File bamFile, String genomeDir)	umms.core.scripture.BuildScriptureCoordinateSpace
BuildScriptureCoordinateSpace(File bamFile, String genomeDir, String outputName, boolean forceStrandedness, TranscriptionRead st, ArgumentMap argMap)	umms.core.scripture.BuildScriptureCoordinateSpace
BuildScriptureCoordinateSpace(File bamFile, String genomeDir, String outputName, boolean forceStrandedness, TranscriptionRead strand, String chr, ArgumentMap argMap)	umms.core.scripture.BuildScriptureCoordinateSpace
compatible(Annotation assembly, Annotation read)	umms.core.scripture.BuildScriptureCoordinateSpace	static
getIsoformMap(Collection< Gene > genes)	umms.core.scripture.BuildScriptureCoordinateSpace	static
getOverlappingGenes(Gene gene, Collection< Gene > allGenes, double minPctOverlap)	umms.core.scripture.BuildScriptureCoordinateSpace	static
getOverlappingGenes(Gene gene, IntervalTree< Gene > allGenesTree, double minPctOverlap)	umms.core.scripture.BuildScriptureCoordinateSpace	static
getPaths()	umms.core.scripture.BuildScriptureCoordinateSpace
hasAnOverlappingGene(Gene gene, IntervalTree< Gene > allGenesTree, double minPctOverlap)	umms.core.scripture.BuildScriptureCoordinateSpace	static
isoformMapContains(Map< Gene, Set< Gene >> isoformMap, Gene gene)	umms.core.scripture.BuildScriptureCoordinateSpace	static
l2a(List< Double > list)	umms.core.scripture.BuildScriptureCoordinateSpace	static
main(String[] args)	umms.core.scripture.BuildScriptureCoordinateSpace	static
memoryStats()	umms.core.scripture.BuildScriptureCoordinateSpace	static
write(String save, Map< String, Collection< Gene >> rtrn)	umms.core.scripture.BuildScriptureCoordinateSpace	static