umms.core.model.JCSAlignmentModel Class Reference

Inheritance diagram for umms.core.model.JCSAlignmentModel:

Collaboration diagram for umms.core.model.JCSAlignmentModel:

Classes
class	AlignmentCount
class	FilteredIterator
class	NodeIterator
class	WrapAlignmentCountIterator

Public Member Functions
	JCSAlignmentModel (String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters, boolean readOrCreatePairedEndBam)
	JCSAlignmentModel ()
	JCSAlignmentModel (String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters, boolean readOrCreatePairedEndBam, TranscriptionRead transcriptionRead)
	JCSAlignmentModel (String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters, boolean readOrCreatePairedEndBam, TranscriptionRead transcriptionRead, boolean fragment)
	JCSAlignmentModel (String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters, boolean readOrCreatePairedEndBam, TranscriptionRead transcriptionRead, String maskedRegionFile)
	JCSAlignmentModel (String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters, boolean readOrCreatePairedEndBam, TranscriptionRead transcriptionRead, boolean fragment, String maskedRegionFile)
	JCSAlignmentModel (String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters)
	JCSAlignmentModel (String bamFile, CoordinateSpace coordinateSpace, Collection< Predicate< Alignment >> readFilters, TranscriptionRead transcriptionRead)
	JCSAlignmentModel (String bamFile, CoordinateSpace coordinateSpace, boolean readOrCreatePairedEndBam)
	JCSAlignmentModel (String bamFile, CoordinateSpace coordinateSpace, boolean readOrCreatePairedEndBam, TranscriptionRead transcriptionRead)
	JCSAlignmentModel (String bamFile, CoordinateSpace coordinateSpace)
	JCSAlignmentModel (String bamFile, CoordinateSpace coordinateSpace, TranscriptionRead transcriptionRead)
SAMFileHeader	getHeader ()
void	computeGlobalStats ()
CloseableIterator< Alignment >	getReadIterator ()
CloseableIterator< Alignment >	getReadIterator (Annotation region)
double	getRefSequenceCounts (String refName)
double	getCount (Annotation window, boolean fullyContained)
double	getCount ()
double	getCount (CloseableIterator< AlignmentCount > iter)
double	getGlobalLambda ()
double	getGlobalLength ()
double	getGlobalPairedFragments ()
EmpiricalDistribution	getReadSizeDistribution (CoordinateSpace coord, int maxSize, int numBins)
EmpiricalDistribution	getReadSizeDistribution (Annotation region, CoordinateSpace coord, int maxSize, int numBins)
double	getMedianReadSize (Annotation region, CoordinateSpace coord, int maxSize, int numBins, boolean fullyContained)
double	getMedianReadSize (Annotation region, CoordinateSpace coord, int maxSize, int numBins)
EmpiricalDistribution	getReadSizeDistribution (Annotation region, CoordinateSpace coord, int maxSize, int numBins, boolean fullyContained)
CloseableIterator< AlignmentCount >	getOverlappingReadCounts (Annotation region, boolean fullyContained)
CloseableIterator< Alignment >	getOverlappingSplicedReads (Annotation region, boolean fullyContained)
CloseableIterator< Alignment >	getOverlappingSplicedReads (String chr)
CloseableIterator< Alignment >	getOverlappingReads (String chr)
int	getBasesCovered (Annotation region, boolean fullyContained)
CloseableIterator< Alignment >	getPermutedAnnotations (Annotation region)
double	getGlobalNumReads ()
double	getGlobalNumReadsReferenceSeqs ()
boolean	isValid (Alignment read)
double	getCount (Annotation window)
boolean	containsReference (String refName)
double	getGlobalCount ()
double	getGlobalCountReferenceSeqs ()
int	size ()
void	addFilter (Predicate< Alignment > filter)
void	addFilters (Collection< Predicate< Alignment >> filters)
WindowScoreIterator< CountScore >	scan (Annotation region, int windowSize, int overlap)
long	getRefSequenceLength (String refName)
Iterator<?extends Window >	windowIterator (int windowSize, int overlap)
double	getRefSequenceLambda (String refName)
Map< String, Integer >	getRefSequenceLengths ()
CoordinateSpace	getCoordinateSpace ()
String	getBamFile ()
int	getBasesCovered (Annotation region)
void	removeFilter (Predicate< Alignment > readFilter)
int	getIntronCounts (Annotation intron)
Map< Alignment, Integer >	getOverlappingReadReplicateCounts (Annotation region, boolean fullyContained)
CloseableIterator< Alignment >	getOverlappingReads (Annotation region, boolean fullyContained)
Annotation	getPeak (Annotation parent, Annotation region, boolean fullyContained)
CloseableIterator< Alignment >	getOverlappingAnnotations (Annotation region, boolean fullyContained)
CloseableIterator< Alignment >	iterator ()
double	getCountExcludingRegion (Annotation region, Annotation excluded)
double	getSplicedCount (Alignments alignments, boolean fullyContained)
double	getAverageCountPerPositionWithThreshold (Gene gene, int minCount)
double	getAverageCountPerPosition (Gene gene)
double[]	getCountsPerPosition (Gene gene)
List< Double >	getCountsStrandedPerPosition (Annotation gene)
double	getCountStrandedExcludingRegion (Annotation region, Annotation excluded)
AlignmentType	getAlignmentType ()

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

Protected Attributes
CoordinateSpace	coordinateSpace

Detailed Description

Serves the purpose of the Generic DataAlignment model and the ContinuousDataAlignmentModel Will populate alignments If a paired end file has unmapped mates, it will be represented by a single end read If both mates are mapped it will be represented as paired end reads Therefore a single model might have both, use flag X to exclude or include only one type This will be a bridge to the analysis modules

Author

skadri

Constructor & Destructor Documentation

umms.core.model.JCSAlignmentModel.JCSAlignmentModel	(	String	bamFile,
		CoordinateSpace	coordinateSpace,
		Collection< Predicate< Alignment >>	readFilters,
		boolean	readOrCreatePairedEndBam
	)

Build with a BAM file Populate the alignment collection

Parameters

bamFile
coordinateSpace
readFilters

Exceptions

IOException

umms.core.model.JCSAlignmentModel.JCSAlignmentModel

(

)

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umms.core.model.JCSAlignmentModel.JCSAlignmentModel	(	String	bamFile,
		CoordinateSpace	coordinateSpace,
		Collection< Predicate< Alignment >>	readFilters,
		boolean	readOrCreatePairedEndBam,
		TranscriptionRead	transcriptionRead
	)

Populate the alignment collection

Parameters

bamFile
coordinateSpace
readFilters

Exceptions

IOException

umms.core.model.JCSAlignmentModel.JCSAlignmentModel	(	String	bamFile,
		CoordinateSpace	coordinateSpace,
		Collection< Predicate< Alignment >>	readFilters,
		boolean	readOrCreatePairedEndBam,
		TranscriptionRead	transcriptionRead,
		boolean	fragment
	)

umms.core.model.JCSAlignmentModel.JCSAlignmentModel	(	String	bamFile,
		CoordinateSpace	coordinateSpace,
		Collection< Predicate< Alignment >>	readFilters,
		boolean	readOrCreatePairedEndBam,
		TranscriptionRead	transcriptionRead,
		String	maskedRegionFile
	)

umms.core.model.JCSAlignmentModel.JCSAlignmentModel	(	String	bamFile,
		CoordinateSpace	coordinateSpace,
		Collection< Predicate< Alignment >>	readFilters,
		boolean	readOrCreatePairedEndBam,
		TranscriptionRead	transcriptionRead,
		boolean	fragment,
		String	maskedRegionFile
	)

Populate the alignment collection

Parameters

bamFile
coordinateSpace
readFilters

Exceptions

IOException

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umms.core.model.JCSAlignmentModel.JCSAlignmentModel	(	String	bamFile,
		CoordinateSpace	coordinateSpace,
		Collection< Predicate< Alignment >>	readFilters
	)

umms.core.model.JCSAlignmentModel.JCSAlignmentModel	(	String	bamFile,
		CoordinateSpace	coordinateSpace,
		Collection< Predicate< Alignment >>	readFilters,
		TranscriptionRead	transcriptionRead
	)

umms.core.model.JCSAlignmentModel.JCSAlignmentModel	(	String	bamFile,
		CoordinateSpace	coordinateSpace,
		boolean	readOrCreatePairedEndBam
	)

umms.core.model.JCSAlignmentModel.JCSAlignmentModel	(	String	bamFile,
		CoordinateSpace	coordinateSpace,
		boolean	readOrCreatePairedEndBam,
		TranscriptionRead	transcriptionRead
	)

umms.core.model.JCSAlignmentModel.JCSAlignmentModel	(	String	bamFile,
		CoordinateSpace	coordinateSpace
	)

umms.core.model.JCSAlignmentModel.JCSAlignmentModel	(	String	bamFile,
		CoordinateSpace	coordinateSpace,
		TranscriptionRead	transcriptionRead
	)

Member Function Documentation

void umms.core.model.JCSAlignmentModel.addFilter

(

Predicate< Alignment >

filter

)

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void umms.core.model.JCSAlignmentModel.addFilters

(

Collection< Predicate< Alignment >>

filters

)

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void umms.core.model.JCSAlignmentModel.computeGlobalStats

(

)

Compute global stats and cache to a file for future use, or read from file if already cached

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boolean umms.core.model.JCSAlignmentModel.containsReference

(

String

refName

)

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AlignmentType umms.core.model.JCSAlignmentModel.getAlignmentType

(

)

Returns the alignment type of the model

Returns

double umms.core.model.JCSAlignmentModel.getAverageCountPerPosition

(

Gene

gene

)

Get the average position level coverage

Parameters

gene

The gene

Returns

The average of all position counts in the gene

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double umms.core.model.JCSAlignmentModel.getAverageCountPerPositionWithThreshold	(	Gene	gene,
		int	minCount
	)

Get average position level coverage of only positions with count above a threshold (denominator excludes positions not passing threshold)

Parameters

gene	The gene
minCount	Min coverage to include a position

Returns

The average of all position counts over threshold in the gene

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String umms.core.model.JCSAlignmentModel.getBamFile

(

)

int umms.core.model.JCSAlignmentModel.getBasesCovered	(	Annotation	region,
		boolean	fullyContained
	)

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int umms.core.model.JCSAlignmentModel.getBasesCovered

(

Annotation

region

)

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CoordinateSpace umms.core.model.JCSAlignmentModel.getCoordinateSpace

(

)

double umms.core.model.JCSAlignmentModel.getCount	(	Annotation	window,
		boolean	fullyContained
	)

Use the coordinate space to decide what is an overlapping read

Parameters

window
fullyContained

Returns

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double umms.core.model.JCSAlignmentModel.getCount

(

)

Use the coordinate space to decide what is an overlapping read Gets the count over the entire genome

Returns

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double umms.core.model.JCSAlignmentModel.getCount

(

CloseableIterator< AlignmentCount >

iter

)

double umms.core.model.JCSAlignmentModel.getCount

(

Annotation

window

)

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double umms.core.model.JCSAlignmentModel.getCountExcludingRegion	(	Annotation	region,
		Annotation	excluded
	)

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double [] umms.core.model.JCSAlignmentModel.getCountsPerPosition

(

Gene

gene

)

This function returns an array list of counts for each position along the specified gene

Parameters

gene

Returns

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List<Double> umms.core.model.JCSAlignmentModel.getCountsStrandedPerPosition

(

Annotation

gene

)

This function returns an array list of counts for each position along the specified gene

Parameters

gene

Returns

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double umms.core.model.JCSAlignmentModel.getCountStrandedExcludingRegion	(	Annotation	region,
		Annotation	excluded
	)

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double umms.core.model.JCSAlignmentModel.getGlobalCount

(

)

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double umms.core.model.JCSAlignmentModel.getGlobalCountReferenceSeqs

(

)

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double umms.core.model.JCSAlignmentModel.getGlobalLambda

(

)

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double umms.core.model.JCSAlignmentModel.getGlobalLength

(

)

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double umms.core.model.JCSAlignmentModel.getGlobalNumReads

(

)

Get total number of reads

Returns

Total read count

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double umms.core.model.JCSAlignmentModel.getGlobalNumReadsReferenceSeqs

(

)

Get total number of reads mapping to the coordinate space

Returns

Total read count on coordinate space

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double umms.core.model.JCSAlignmentModel.getGlobalPairedFragments

(

)

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SAMFileHeader umms.core.model.JCSAlignmentModel.getHeader

(

)

Returns the SAM file header for this reader

Returns

int umms.core.model.JCSAlignmentModel.getIntronCounts

(

Annotation

intron

)

This will count the number of spliced reads with exactly this intron

Parameters

intron

the intron to count

Returns

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double umms.core.model.JCSAlignmentModel.getMedianReadSize	(	Annotation	region,
		CoordinateSpace	coord,
		int	maxSize,
		int	numBins,
		boolean	fullyContained
	)

Get the median of all read (or fragment) sizes in an annotation

Parameters

region	The annotation in which to count read sizes
coord	Coordinate space in which to compute read sizes
maxSize	The maximum read size to check for
numBins	The number of bins for histogram
fullyContained	Count fully contained reads/fragments only

Returns

Distribution of read sizes with respect to coordinate space

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double umms.core.model.JCSAlignmentModel.getMedianReadSize	(	Annotation	region,
		CoordinateSpace	coord,
		int	maxSize,
		int	numBins
	)

Get the median of all read (or fragment) sizes in an annotation

Parameters

region	The annotation in which to count read sizes
coord	Coordinate space in which to compute read sizes
maxSize	The maximum read size to check for
numBins	The number of bins for histogram

Returns

Distribution of read sizes with respect to coordinate space

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CloseableIterator<Alignment> umms.core.model.JCSAlignmentModel.getOverlappingAnnotations	(	Annotation	region,
		boolean	fullyContained
	)

CloseableIterator<AlignmentCount> umms.core.model.JCSAlignmentModel.getOverlappingReadCounts	(	Annotation	region,
		boolean	fullyContained
	)

Return the reads that overlap with this region in coordinate space If the Alignment model has a strand which is NOT unstranded, then returns stranded counts

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Map<Alignment, Integer> umms.core.model.JCSAlignmentModel.getOverlappingReadReplicateCounts	(	Annotation	region,
		boolean	fullyContained
	)

Get number of replicates of each read overlapping the region

Parameters

region	The region
fullyContained	Count fully contained reads only

Returns

For each unique read position, the number of replicates

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CloseableIterator<Alignment> umms.core.model.JCSAlignmentModel.getOverlappingReads

(

String

chr

)

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CloseableIterator<Alignment> umms.core.model.JCSAlignmentModel.getOverlappingReads	(	Annotation	region,
		boolean	fullyContained
	)

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CloseableIterator<Alignment> umms.core.model.JCSAlignmentModel.getOverlappingSplicedReads	(	Annotation	region,
		boolean	fullyContained
	)

Return the reads that overlap with this region in coordinate space

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CloseableIterator<Alignment> umms.core.model.JCSAlignmentModel.getOverlappingSplicedReads

(

String

chr

)

Return the reads that overlap with this region in coordinate space

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Annotation umms.core.model.JCSAlignmentModel.getPeak	(	Annotation	parent,
		Annotation	region,
		boolean	fullyContained
	)

Get the span covered by all reads overlapping a region

Parameters

parent	Parent annotation of the region of interest
region	The region of interest
fullyContained	Fully contained reads only

Returns

The subregion of the parent gene enclosing all reads overlapping the region or null if no overlappers

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CloseableIterator<Alignment> umms.core.model.JCSAlignmentModel.getPermutedAnnotations

(

Annotation

region

)

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CloseableIterator<Alignment> umms.core.model.JCSAlignmentModel.getReadIterator

(

)

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CloseableIterator<Alignment> umms.core.model.JCSAlignmentModel.getReadIterator

(

Annotation

region

)

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EmpiricalDistribution umms.core.model.JCSAlignmentModel.getReadSizeDistribution	(	CoordinateSpace	coord,
		int	maxSize,
		int	numBins
	)

Get the distribution of all read (or fragment) sizes with respect to a coordinate space

Parameters

coord	The coordinate space
maxSize	The maximum read size to consider
numBins	The number of bins for histogram

Returns

Distribution of read sizes with respect to coordinate space

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EmpiricalDistribution umms.core.model.JCSAlignmentModel.getReadSizeDistribution	(	Annotation	region,
		CoordinateSpace	coord,
		int	maxSize,
		int	numBins
	)

Get the distribution of read (or fragment) sizes in an annotation

Parameters

region	The annotation in which to count read sizes
coord	Coordinate space in which to compute read sizes
maxSize	The maximum read size to check for
numBins	The number of bins for histogram

Returns

Distribution of read sizes with respect to coordinate space

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EmpiricalDistribution umms.core.model.JCSAlignmentModel.getReadSizeDistribution	(	Annotation	region,
		CoordinateSpace	coord,
		int	maxSize,
		int	numBins,
		boolean	fullyContained
	)

Get the distribution of read (or fragment) sizes in an annotation

Parameters

region	The annotation in which to count read sizes
coord	Coordinate space in which to compute read sizes
maxSize	The maximum read size to check for
numBins	The number of bins for histogram
fullyContained	Count fully contained reads/fragments only

Returns

Distribution of read sizes with respect to coordinate space

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double umms.core.model.JCSAlignmentModel.getRefSequenceCounts

(

String

refName

)

This function calculates the number of proper paired end reads over the entire coordinate space

Author

skadri

Returns

Returns the counts for the specified reference sequence

Parameters

refName

Returns

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double umms.core.model.JCSAlignmentModel.getRefSequenceLambda

(

String

refName

)

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long umms.core.model.JCSAlignmentModel.getRefSequenceLength

(

String

refName

)

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Map<String, Integer> umms.core.model.JCSAlignmentModel.getRefSequenceLengths

(

)

Get the lengths of the reference sequences

Returns

Map associating each reference name with sequence length

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double umms.core.model.JCSAlignmentModel.getSplicedCount	(	Alignments	alignments,
		boolean	fullyContained
	)

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boolean umms.core.model.JCSAlignmentModel.isValid

(

Alignment

read

)

CloseableIterator<Alignment> umms.core.model.JCSAlignmentModel.iterator

(

)

static void umms.core.model.JCSAlignmentModel.main ( String[]  args ) throws IOException

static

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void umms.core.model.JCSAlignmentModel.removeFilter

(

Predicate< Alignment >

readFilter

)

Removes a read filter from the set

Parameters

readFilter

to remove

WindowScoreIterator<CountScore> umms.core.model.JCSAlignmentModel.scan	(	Annotation	region,
		int	windowSize,
		int	overlap
	)

int umms.core.model.JCSAlignmentModel.size

(

)

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Iterator<? extends Window> umms.core.model.JCSAlignmentModel.windowIterator	(	int	windowSize,
		int	overlap
	)

Iterate through the whole coordinate space in windows and score them using the provided window processor

Parameters

windowSize

size of the windows to score

Member Data Documentation

CoordinateSpace umms.core.model.JCSAlignmentModel.coordinateSpace

protected

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

• java/umms/core/model/JCSAlignmentModel.java