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

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

ANNOTATION	broad.pda.seq.rap.GenomeCommandLineProgram
ANNOTATION_FILE	broad.pda.seq.rap.rna.CountReads
CONTROL	broad.pda.seq.rap.rna.TranscriptomeScoringProgram
COORD_SPACE	broad.pda.seq.rap.GenomeCommandLineProgram
coordinateSpace	broad.pda.seq.rap.GenomeCommandLineProgram	protected
customCommandLineValidation()	broad.pda.seq.rap.rna.TranscriptomeScoringProgram	protected
doWork()	broad.pda.seq.rap.rna.CountReads	protected
GENE	broad.pda.seq.rap.GenomeCommandLineProgram
GENE_BED	broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
getCoordinateSpace()	broad.pda.seq.rap.GenomeCommandLineProgram	protected
getGenes()	broad.pda.seq.rap.GenomeCommandLineProgram
getGenomicSpace()	broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram	protected
getRegions()	broad.pda.seq.rap.GenomeCommandLineProgram
getRegionSet()	broad.pda.seq.rap.GenomeCommandLineProgram
getRegionsMap()	broad.pda.seq.rap.GenomeCommandLineProgram
getTranscriptomeSpace()	broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram	protected
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.TranscriptomeCommandLineProgram	protected
loadRNAAlignmentModel(File bamFile, boolean pairedEnd)	broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
main(final String[] args)	broad.pda.seq.rap.rna.CountReads	static
MASK_FILE	broad.pda.seq.rap.GenomeCommandLineProgram
MAX_FRAGMENT_LENGTH	broad.pda.seq.rap.GenomeCommandLineProgram
MIN_MAPPING_QUALITY	broad.pda.seq.rap.GenomeCommandLineProgram
OUTPUT	broad.pda.seq.rap.rna.CountReads
PAIRED_END	broad.pda.seq.rap.rna.TranscriptomeScoringProgram
PCT_MASKED_ALLOWED	broad.pda.seq.rap.GenomeCommandLineProgram
REGION	broad.pda.seq.rap.GenomeCommandLineProgram
SCORE	broad.pda.seq.rap.rna.TranscriptomeScoringProgram
SIZES	broad.pda.seq.rap.GenomeCommandLineProgram
TARGET	broad.pda.seq.rap.rna.TranscriptomeScoringProgram
TRANSCRIPTION_READ	broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
ts	broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram	protected
USAGE	broad.pda.seq.rap.rna.CountReads