broad.pda.seq.rap.SlideAndCalculate Class Reference

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

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

Public Member Functions
Iterator<?extends WindowScore >	getWindowScoreIterator () throws IOException
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)

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). This is currently written for Genomic Space analyses but should be modified to allow other coordinate systems."
int	WINDOW
int	OVERLAP
File	OUTPUT
Double	RPKM_RATIO_OFFSET = RatioScore.RPKM_OFFSET
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
Protected Attributes inherited from broad.pda.seq.rap.GenomeCommandLineProgram
CoordinateSpace	coordinateSpace

Member Function Documentation

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

protected

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Iterator<? extends WindowScore> broad.pda.seq.rap.SlideAndCalculate.getWindowScoreIterator

(

)

throws IOException

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

static

Stock main method.

Parameters

args	main arguments

Member Data Documentation

File broad.pda.seq.rap.SlideAndCalculate.OUTPUT

int broad.pda.seq.rap.SlideAndCalculate.OVERLAP

Double broad.pda.seq.rap.SlideAndCalculate.RPKM_RATIO_OFFSET = RatioScore.RPKM_OFFSET

String broad.pda.seq.rap.SlideAndCalculate.USAGE = "Slides across the genome and counts reads (or calculates ratios for two models). This is currently written for Genomic Space analyses but should be modified to allow other coordinate systems."

int broad.pda.seq.rap.SlideAndCalculate.WINDOW

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

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