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broad.pda.seq.rap.rna.TranscriptomeScoringProgram Member List

This is the complete list of members for broad.pda.seq.rap.rna.TranscriptomeScoringProgram, including all inherited members.

ANNOTATIONbroad.pda.seq.rap.GenomeCommandLineProgram
CONTROLbroad.pda.seq.rap.rna.TranscriptomeScoringProgram
COORD_SPACEbroad.pda.seq.rap.GenomeCommandLineProgram
coordinateSpacebroad.pda.seq.rap.GenomeCommandLineProgramprotected
customCommandLineValidation()broad.pda.seq.rap.rna.TranscriptomeScoringProgramprotected
GENEbroad.pda.seq.rap.GenomeCommandLineProgram
GENE_BEDbroad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
getCoordinateSpace()broad.pda.seq.rap.GenomeCommandLineProgramprotected
getGenes()broad.pda.seq.rap.GenomeCommandLineProgram
getGenomicSpace()broad.pda.seq.rap.rna.TranscriptomeCommandLineProgramprotected
getRegions()broad.pda.seq.rap.GenomeCommandLineProgram
getRegionSet()broad.pda.seq.rap.GenomeCommandLineProgram
getRegionsMap()broad.pda.seq.rap.GenomeCommandLineProgram
getTranscriptomeSpace()broad.pda.seq.rap.rna.TranscriptomeCommandLineProgramprotected
getWindowProcessor()broad.pda.seq.rap.rna.TranscriptomeScoringProgram
getWindowProcessor(AnnotationCollection<?extends Annotation > target, AnnotationCollection<?extends Annotation > control)broad.pda.seq.rap.rna.TranscriptomeScoringProgram
isGenomicSpace()broad.pda.seq.rap.GenomeCommandLineProgram
loadAlignmentModel(File bamFile, boolean pairedEnd)broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
broad::pda::seq::rap::GenomeCommandLineProgram.loadAlignmentModel(File bamFile)broad.pda.seq.rap.GenomeCommandLineProgram
loadCoordinateSpace()broad.pda.seq.rap.rna.TranscriptomeCommandLineProgramprotected
loadRNAAlignmentModel(File bamFile, boolean pairedEnd)broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
MASK_FILEbroad.pda.seq.rap.GenomeCommandLineProgram
MAX_FRAGMENT_LENGTHbroad.pda.seq.rap.GenomeCommandLineProgram
MIN_MAPPING_QUALITYbroad.pda.seq.rap.GenomeCommandLineProgram
PAIRED_ENDbroad.pda.seq.rap.rna.TranscriptomeScoringProgram
PCT_MASKED_ALLOWEDbroad.pda.seq.rap.GenomeCommandLineProgram
REGIONbroad.pda.seq.rap.GenomeCommandLineProgram
SCOREbroad.pda.seq.rap.rna.TranscriptomeScoringProgram
SIZESbroad.pda.seq.rap.GenomeCommandLineProgram
TARGETbroad.pda.seq.rap.rna.TranscriptomeScoringProgram
TRANSCRIPTION_READbroad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
tsbroad.pda.seq.rap.rna.TranscriptomeCommandLineProgramprotected
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