broad.pda.seq.rap.GenomeCommandLineProgram Class Reference

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Public Member Functions
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
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 () throws IOException
CoordinateSpace	getCoordinateSpace ()

Protected Attributes
CoordinateSpace	coordinateSpace

Detailed Description

Author

engreitz Class used to run various analyses on sequencing data alignments in genomic or transcriptome space. Automatically filters improper pairs, chimeric reads and PCR duplicates

Member Function Documentation

String [] broad.pda.seq.rap.GenomeCommandLineProgram.customCommandLineValidation ( )

protected

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CoordinateSpace broad.pda.seq.rap.GenomeCommandLineProgram.getCoordinateSpace ( )

protected

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Annotation broad.pda.seq.rap.GenomeCommandLineProgram.getGenes

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List<Annotation> broad.pda.seq.rap.GenomeCommandLineProgram.getRegions

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AnnotationList<Annotation> broad.pda.seq.rap.GenomeCommandLineProgram.getRegionSet

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Map<String,Annotation> broad.pda.seq.rap.GenomeCommandLineProgram.getRegionsMap

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Boolean broad.pda.seq.rap.GenomeCommandLineProgram.isGenomicSpace

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AlignmentModel broad.pda.seq.rap.GenomeCommandLineProgram.loadAlignmentModel

(

File

bamFile

)

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

void broad.pda.seq.rap.GenomeCommandLineProgram.loadCoordinateSpace ( ) throws IOException

protected

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Member Data Documentation

String broad.pda.seq.rap.GenomeCommandLineProgram.ANNOTATION = "/seq/lincRNA/Shari/Annotations/RefSeq_LincV3_ChromatinWithNames_nonrandom_collapsed_overlappers.bed"

String broad.pda.seq.rap.GenomeCommandLineProgram.COORD_SPACE = "genomic"

CoordinateSpace broad.pda.seq.rap.GenomeCommandLineProgram.coordinateSpace

protected

String broad.pda.seq.rap.GenomeCommandLineProgram.GENE = null

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

Integer broad.pda.seq.rap.GenomeCommandLineProgram.MAX_FRAGMENT_LENGTH = 10000

Integer broad.pda.seq.rap.GenomeCommandLineProgram.MIN_MAPPING_QUALITY = 30

double broad.pda.seq.rap.GenomeCommandLineProgram.PCT_MASKED_ALLOWED = 50.0

String broad.pda.seq.rap.GenomeCommandLineProgram.REGION = null

String broad.pda.seq.rap.GenomeCommandLineProgram.SIZES = "/seq/lincRNA/data/mm9/sizes"

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

• java/broad/pda/seq/rap/GenomeCommandLineProgram.java