Inheritance diagram for broad.pda.seq.rap.SlideAndCount:

Collaboration diagram for broad.pda.seq.rap.SlideAndCount:

Static Public Member Functions
static void	main (final String[] args)

Public Attributes
String	USAGE = "Slides across the genome and counts reads (or calculates ratios for two models)."

Integer	WINDOW = null

Integer	OVERLAP = null

File	OUTPUT

Public Attributes inherited from broad.pda.seq.rap.GenomeScoringProgram
File	TARGET

File	CONTROL = null

String	SCORE = "count"

boolean	PAIRED_END =true

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
int	doWork ()

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

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

void	loadCoordinateSpace () throws IOException

CoordinateSpace	getCoordinateSpace ()

Additional Inherited Members
Public Member Functions inherited from broad.pda.seq.rap.GenomeScoringProgram
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.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)

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

Member Function Documentation

int broad.pda.seq.rap.SlideAndCount.doWork ( )

protected

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static void broad.pda.seq.rap.SlideAndCount.main ( final String[] args )

static

Stock main method.

Parameters

args	main arguments

Member Data Documentation

File broad.pda.seq.rap.SlideAndCount.OUTPUT

Integer broad.pda.seq.rap.SlideAndCount.OVERLAP = null

String broad.pda.seq.rap.SlideAndCount.USAGE = "Slides across the genome and counts reads (or calculates ratios for two models)."

Integer broad.pda.seq.rap.SlideAndCount.WINDOW = null

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