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

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

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

Public Attributes
String	USAGE = "Shuffle reads in a SAM or BAM file, avoiding unmappable regions."

File	INPUT

File	OUTPUT

Integer	PERMUTATIONS = 1

Integer	RANDOM_SEED = null

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.GenomeCommandLineProgram
String[]	customCommandLineValidation ()

void	loadCoordinateSpace () throws IOException

CoordinateSpace	getCoordinateSpace ()

Additional Inherited Members
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.ShuffleBAM.doWork ( )

protected

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

static

Stock main method.

Parameters

args	main arguments

Member Data Documentation

File broad.pda.seq.rap.ShuffleBAM.INPUT

File broad.pda.seq.rap.ShuffleBAM.OUTPUT

Integer broad.pda.seq.rap.ShuffleBAM.PERMUTATIONS = 1

Integer broad.pda.seq.rap.ShuffleBAM.RANDOM_SEED = null

String broad.pda.seq.rap.ShuffleBAM.USAGE = "Shuffle reads in a SAM or BAM file, avoiding unmappable regions."

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