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

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

Public Member Functions
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	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 ()

void	loadCoordinateSpace ()

GenomicSpace	getGenomicSpace ()

TranscriptomeSpace	getTranscriptomeSpace ()

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

void	loadCoordinateSpace () throws IOException

CoordinateSpace	getCoordinateSpace ()

Protected Attributes
TranscriptomeSpace	ts

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

Member Function Documentation

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

protected

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GenomicSpace broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram.getGenomicSpace ( )

protected

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TranscriptomeSpace broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram.getTranscriptomeSpace ( )

protected

AlignmentModel broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram.loadAlignmentModel	(	File	bamFile,
		boolean	pairedEnd
	)

void broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram.loadCoordinateSpace ( )

protected

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AlignmentModel broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram.loadRNAAlignmentModel	(	File	bamFile,
		boolean	pairedEnd
	)

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Member Data Documentation

File broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram.GENE_BED

TranscriptionRead broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram.TRANSCRIPTION_READ =TranscriptionRead.SECOND_OF_PAIR

TranscriptomeSpace broad.pda.seq.rap.rna.TranscriptomeCommandLineProgram.ts

protected

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