broad.pda.seq.rap.CountReads Class Reference

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

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

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

Public Attributes
String	USAGE = "Counts reads overlapping the provided BED files. This is currently written for Genomic Space analyses but should be modified to allow other coordinate systems."
File	ANNOTATION_FILE
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.CountReads.doWork ( )

protected

Here is the call graph for this function:

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

static

Stock main method.

Parameters

args	main arguments

Member Data Documentation

File broad.pda.seq.rap.CountReads.ANNOTATION_FILE

File broad.pda.seq.rap.CountReads.OUTPUT

String broad.pda.seq.rap.CountReads.USAGE = "Counts reads overlapping the provided BED files. This is currently written for Genomic Space analyses but should be modified to allow other coordinate systems."

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

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