Inheritance diagram for broad.pda.seq.rap.rna.TranscriptomeScoringProgram:

Collaboration diagram for broad.pda.seq.rap.rna.TranscriptomeScoringProgram:

Public Member Functions
WindowProcessor<?extends WindowScore >	getWindowProcessor ()

WindowProcessor<?extends WindowScore >	getWindowProcessor (AnnotationCollection<?extends Annotation > target, AnnotationCollection<?extends Annotation > control)

Public Member Functions inherited from broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
AlignmentModel	loadRNAAlignmentModel (File bamFile, boolean pairedEnd)

AlignmentModel	loadAlignmentModel (File bamFile, boolean pairedEnd)

Public Member Functions inherited from broad.pda.seq.rap.GenomeCommandLineProgram
List< Annotation >	getRegions ()

Map< String, Annotation >	getRegionsMap ()

AnnotationList< Annotation >	getRegionSet ()

Annotation	getGenes ()

Boolean	isGenomicSpace ()

AlignmentModel	loadAlignmentModel (File bamFile)

AlignmentModel	loadAlignmentModel (File bamFile, boolean pairedEnd)

Public Attributes
File	TARGET

File	CONTROL = null

String	SCORE = "count"

boolean	PAIRED_END =true

Public Attributes inherited from broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
File	GENE_BED

TranscriptionRead	TRANSCRIPTION_READ =TranscriptionRead.SECOND_OF_PAIR

Public Attributes inherited from broad.pda.seq.rap.GenomeCommandLineProgram
String	SIZES = "/seq/lincRNA/data/mm9/sizes"

String	MASK_FILE = "/seq/mguttman/ChIPData/MaskFiles/MM9Segments/all.mask.mouse.n36.d2.bin"

double	PCT_MASKED_ALLOWED = 50.0

String	REGION = null

String	GENE = null

Integer	MAX_FRAGMENT_LENGTH = 10000

Integer	MIN_MAPPING_QUALITY = 30

String	COORD_SPACE = "genomic"

String	ANNOTATION = "/seq/lincRNA/Shari/Annotations/RefSeq_LincV3_ChromatinWithNames_nonrandom_collapsed_overlappers.bed"

Protected Member Functions
String[]	customCommandLineValidation ()

Protected Member Functions inherited from broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
String[]	customCommandLineValidation ()

void	loadCoordinateSpace ()

GenomicSpace	getGenomicSpace ()

TranscriptomeSpace	getTranscriptomeSpace ()

Protected Member Functions inherited from broad.pda.seq.rap.GenomeCommandLineProgram
String[]	customCommandLineValidation ()

void	loadCoordinateSpace () throws IOException

CoordinateSpace	getCoordinateSpace ()

Additional Inherited Members
Protected Attributes inherited from broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram
TranscriptomeSpace	ts

Protected Attributes inherited from broad.pda.seq.rap.GenomeCommandLineProgram
CoordinateSpace	coordinateSpace

Member Function Documentation

String [] broad.pda.seq.rap.rna.TranscriptomeScoringProgram.customCommandLineValidation ( )

protected

WindowProcessor<? extends WindowScore> broad.pda.seq.rap.rna.TranscriptomeScoringProgram.getWindowProcessor ( )

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WindowProcessor<? extends WindowScore> broad.pda.seq.rap.rna.TranscriptomeScoringProgram.getWindowProcessor	(	AnnotationCollection<?extends Annotation >	target,
		AnnotationCollection<?extends Annotation >	control
	)

Member Data Documentation

File broad.pda.seq.rap.rna.TranscriptomeScoringProgram.CONTROL = null

boolean broad.pda.seq.rap.rna.TranscriptomeScoringProgram.PAIRED_END =true

String broad.pda.seq.rap.rna.TranscriptomeScoringProgram.SCORE = "count"

File broad.pda.seq.rap.rna.TranscriptomeScoringProgram.TARGET

The documentation for this class was generated from the following file: