broad.pda.seq.segmentation.GenericAlignmentDataModel Class Reference

Inheritance diagram for broad.pda.seq.segmentation.GenericAlignmentDataModel:

Collaboration diagram for broad.pda.seq.segmentation.GenericAlignmentDataModel:

Classes
class	EmptyCloseableIterator

Public Member Functions
	GenericAlignmentDataModel (String filename, String lengthFile, boolean upweightSplices, double minMappingQuality, boolean removeDuplicatesFlag, boolean weighReadCounts, String strand, boolean loadPairsAsFragments) throws IOException
	GenericAlignmentDataModel (String filename, String lengthFile, boolean upweightSplices, double minMappingQuality) throws IOException
	GenericAlignmentDataModel (String filename, String lengthFile) throws IOException
	GenericAlignmentDataModel (String filename, String lengthFile, int minMappingQuality) throws IOException
	GenericAlignmentDataModel (String filename, String lengthFile, boolean upweightSplices) throws IOException
	GenericAlignmentDataModel (String filename, String lengthFile, boolean upweightSplices, int minMappingQuality, boolean removeDuplicatesFlag) throws IOException
	GenericAlignmentDataModel (String filename, String lengthFile, int minMappingQuality, boolean removeDuplicatesFlag) throws IOException
	GenericAlignmentDataModel (String filename, String lengthFile, boolean removeDuplicatesFlag, boolean weighReadCounts) throws IOException
	GenericAlignmentDataModel (String filename, String lengthFile, boolean upweightSplices, boolean removeDuplicatesFlag, boolean weighReadCounts) throws IOException
	GenericAlignmentDataModel (String filename, String lengthFile, boolean upweightSplices, int minMappingQuality, boolean removeDuplicatesFlag, boolean weighReadCounts) throws IOException
	GenericAlignmentDataModel (String filename, String lengthFile, boolean upweightSplices, int minMappingQuality, boolean removeDuplicatesFlag, boolean weighReadCounts, String strand) throws IOException
CloseableIterator< Alignment >	getAnnotationOverlappingRegion (Annotation align) throws IOException
double	getBasesCoveredPerAlignment (Gene gene, IntervalTree< Alignment > tree, int EF)
double	getCountsPerAlignmentFullyContained (Gene gene, IntervalTree< Alignment > tree, int EF)
int	getBasesCovered (Annotation region, int EF) throws IOException
Gene	getPeak (Gene gene, Gene startCodon, IntervalTree< Alignment > tree, int EF)
Map< String, Integer >	getChrLengths ()
int	getChrLength (String chr)
CloseableIterator< Alignment >	getChrReadIterator (String chromosome) throws IOException
int	getChunkEnd ()
int	getChunkStart ()
double	getCounts (String chr) throws IOException
double	getCountsOfUniqueOverlappers (Annotation target, Annotation exclude, IntervalTree< Alignment > tree, int EF)
double	getCountsOfUniqueOverlappers (Annotation target, Gene exclude, IntervalTree< Alignment > tree, int EF)
double	getCountsOnBase (String chr, int index) throws IOException
double	getCountsOnWindow (String chr, int startIndex, int endIndex) throws IOException
double	getCountsPerAlignmentUncached (String chr, int startIndex, int endIndex) throws IOException
double	getCountsPerAlignment (Annotation align, int EF) throws IOException
double	getCountsPerAlignment (Annotation align) throws IOException
double	getCountsPerAlignment (Annotation align, IntervalTree< Alignment > tree, int EF)
boolean	loadedPairsAsFragments ()
double	getCountsPerAlignmentForPolyA (Annotation align, int EF) throws IOException
double	getCountsPerAlignment (Gene gene, IntervalTree< Alignment > tree, int EF)
double	getCountsPerAnnotationtranded (Gene gene, IntervalTree< Alignment > tree, int EF, String orientation)
double	getCountsPerAlignment (Annotation[] Annotation, IntervalTree< Alignment > tree, int EF)
double	getCountsPerAlignment (Annotation[] Annotation, int EF) throws IOException
double	getCountsPerAlignment (Annotation align, Map< String, IntervalTree< Annotation >> goodExonTree, IntervalTree< Alignment > tree, int extensionFactor)
double	getCountsPerAlignmentWithSameEndpointForPolyA (Annotation align, int EF, boolean polyAIsOnRight, int typicalOriginalAlignmentLength, int maxDistanceFromOriginalAlignmentEndpoint) throws IOException
int	getCountsWithinExons (Annotation align, IntervalTree< Alignment > tree, int EF)
int	getCountsWithinExons (Annotation align, Iterator< Alignment > iter, int EF)
Iterator< Annotation >	getExonAnnotationOverlappingRegion (Annotation align) throws IOException
Iterator< Annotation >	getExonAnnotationOverlappingRegion (IntervalTree< Alignment > tree)
IntervalTree< Annotation >	getFullIntervalTreeAsAnnotation (String chr) throws IOException
GeneCounts	getGeneCounts (Gene gene, int extensionFactor) throws IOException
String	getModelFilePath ()
IntervalTree< Alignment >	getIntervalTree (String chr, int start, int end) throws IOException
IntervalTree< Alignment >	getIntervalTreeCached (String chr, int start, int end) throws IOException
IntervalTree< Alignment >	getIntervalTreeTruncated (String chr, int start, int end) throws IOException
IntervalTree< Alignment >	getIntervalTreeTruncatedCached (String chromosome, int start, int end) throws IOException
double	getMinimumMappingQuality ()
double	getNumberOfSplicedReads (Annotation align) throws IOException
double	getNumberOfSplicedReads ()
Collection< Annotation >	getOverlappingRegions (String chr) throws IOException
CloseableIterator< Alignment >	getReadIterator ()
CloseableIterator< Alignment >	getReadIterator (Annotation region) throws IOException
SAMFileHeader	getSamHeader () throws IOException
Collection< Annotation >	getSplicedReadExons (String chr) throws IOException
void	setExtensionFactor (int extensionFactor)
Map< Annotation, Integer >	getSplicedReads (Annotation align) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation align, final int minIntronSize, final int maxIntronSize, int minNumIntrons, Sequence chrSeq) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation align, final int minIntronSize, final int maxIntronSize) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation region, Predicate< Annotation > filter) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation region, Collection< Predicate< Annotation >> filters, int minNumIntrons) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation region, Collection< Predicate< Annotation >> filters, int minNumIntrons, Sequence chrSeq) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation region, Collection< Predicate< Annotation >> filters) throws IOException
Map< Annotation, Integer >	getSplicedReads (Annotation region, Collection< Predicate< Annotation >> filters, Sequence chrSeq) throws IOException
Map< Annotation, Integer >	getSplicedReads (int minIntronSize, int maxIntronSize) throws IOException
double	getSpliceWeightFactor ()
double[]	getTotalNumberOfMappedReads ()
double[]	getTotalNumberOfMappedStrandedReads ()
double	getTotalNumberOfStrandedReads ()
double	getTotalNumberOfReads ()
double	getWeight () throws IOException
void	setChunkSize (int chunkSize)
void	setMinimumMappingQuality (double minimumMappingQual)
void	setNegativeStranded ()
void	setSecondRead ()
void	setFirstRead ()
void	setNormalizationStrategy (ReadCountNormalizer normalizer)
void	setPositiveStranded ()
boolean	hasNextExon (String chr) throws IOException
boolean	isPositiveStranded ()
boolean	isNegativeStranded ()
boolean	isStranded ()
boolean	passes (Gene gene, IntervalTree< Alignment > tree, int EF, double cutoff)
long	passesCutoff (Annotation align, IntervalTree< Alignment > tree, int EF, double threshold)
void	resetTreeCache (String chr)
void	resetTreeCache ()
void	restartIterator ()
void	unsetStranded ()
Gene	updateGeneByFirstCounts (Gene gene, IntervalTree< Alignment > tree, int EF)
void	setRemoveDuplicatesFlag (boolean flag)
void	setWeighReadCountsFlag (boolean flag)
double	countReads (Alignment record)
Map< String, Integer >	getChromosomeLengths ()
int	getChromosomeLength (String chr)
CloseableIterator< Alignment >	getChromosomeReadIterator (String chromosome) throws IOException
double	getScorePerAlignmentFromCache (Gene window, IntervalTree< Alignment > chunkAlignmentTree, int extensionFactor)
void	clearFullIntervalTreeAsAlignmentsCached (String chr)
Public Member Functions inherited from broad.pda.seq.segmentation.AlignmentDataModel
Map< Annotation, Integer >	getSplicedReads (Annotation align, int minIntronSize, int maxIntronSize) throws IOException

Constructor & Destructor Documentation

broad.pda.seq.segmentation.GenericAlignmentDataModel.GenericAlignmentDataModel	(	String	filename,
		String	lengthFile,
		boolean	upweightSplices,
		double	minMappingQuality,
		boolean	removeDuplicatesFlag,
		boolean	weighReadCounts,
		String	strand,
		boolean	loadPairsAsFragments
	)		throws IOException

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broad.pda.seq.segmentation.GenericAlignmentDataModel.GenericAlignmentDataModel	(	String	filename,
		String	lengthFile,
		boolean	upweightSplices,
		double	minMappingQuality
	)		throws IOException

broad.pda.seq.segmentation.GenericAlignmentDataModel.GenericAlignmentDataModel	(	String	filename,
		String	lengthFile
	)		throws IOException

broad.pda.seq.segmentation.GenericAlignmentDataModel.GenericAlignmentDataModel	(	String	filename,
		String	lengthFile,
		int	minMappingQuality
	)		throws IOException

broad.pda.seq.segmentation.GenericAlignmentDataModel.GenericAlignmentDataModel	(	String	filename,
		String	lengthFile,
		boolean	upweightSplices
	)		throws IOException

broad.pda.seq.segmentation.GenericAlignmentDataModel.GenericAlignmentDataModel	(	String	filename,
		String	lengthFile,
		boolean	upweightSplices,
		int	minMappingQuality,
		boolean	removeDuplicatesFlag
	)		throws IOException

broad.pda.seq.segmentation.GenericAlignmentDataModel.GenericAlignmentDataModel	(	String	filename,
		String	lengthFile,
		int	minMappingQuality,
		boolean	removeDuplicatesFlag
	)		throws IOException

broad.pda.seq.segmentation.GenericAlignmentDataModel.GenericAlignmentDataModel	(	String	filename,
		String	lengthFile,
		boolean	removeDuplicatesFlag,
		boolean	weighReadCounts
	)		throws IOException

broad.pda.seq.segmentation.GenericAlignmentDataModel.GenericAlignmentDataModel	(	String	filename,
		String	lengthFile,
		boolean	upweightSplices,
		boolean	removeDuplicatesFlag,
		boolean	weighReadCounts
	)		throws IOException

broad.pda.seq.segmentation.GenericAlignmentDataModel.GenericAlignmentDataModel	(	String	filename,
		String	lengthFile,
		boolean	upweightSplices,
		int	minMappingQuality,
		boolean	removeDuplicatesFlag,
		boolean	weighReadCounts
	)		throws IOException

broad.pda.seq.segmentation.GenericAlignmentDataModel.GenericAlignmentDataModel	(	String	filename,
		String	lengthFile,
		boolean	upweightSplices,
		int	minMappingQuality,
		boolean	removeDuplicatesFlag,
		boolean	weighReadCounts,
		String	strand
	)		throws IOException

Member Function Documentation

void broad.pda.seq.segmentation.GenericAlignmentDataModel.clearFullIntervalTreeAsAlignmentsCached

(

String

chr

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

double broad.pda.seq.segmentation.GenericAlignmentDataModel.countReads

(

Alignment

record

)

Author

: skadri This function will calculate the count value for an alignment read record based on the alue of the weigh ReadCounts flag

Parameters

record

Returns

Count value for alignment

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CloseableIterator<Alignment> broad.pda.seq.segmentation.GenericAlignmentDataModel.getAnnotationOverlappingRegion

(

Annotation

align

)

throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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int broad.pda.seq.segmentation.GenericAlignmentDataModel.getBasesCovered	(	Annotation	region,
		int	EF
	)		throws IOException

Author

Jesse Engreitz

Parameters

region	region of interest
EF	extension factor

Returns

Number of bases covered by at least one read Warning: This is not a very efficient function with lots of reads TODO rewrite using merge

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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double broad.pda.seq.segmentation.GenericAlignmentDataModel.getBasesCoveredPerAlignment	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

int broad.pda.seq.segmentation.GenericAlignmentDataModel.getChrLength

(

String

chr

)

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Map<String, Integer> broad.pda.seq.segmentation.GenericAlignmentDataModel.getChrLengths

(

)

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int broad.pda.seq.segmentation.GenericAlignmentDataModel.getChromosomeLength

(

String

chr

)

Get length of a chromosome

Parameters

chr

Returns

Implements broad.pda.seq.segmentation.AlignmentDataModel.

Map<String, Integer> broad.pda.seq.segmentation.GenericAlignmentDataModel.getChromosomeLengths

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

CloseableIterator<Alignment> broad.pda.seq.segmentation.GenericAlignmentDataModel.getChromosomeReadIterator

(

String

chromosome

)

throws IOException

Parameters

the	chromosome over which to iterate

Returns

CloseableIterator over all reads mapped to the given Chromosome

Implements broad.pda.seq.segmentation.AlignmentDataModel.

CloseableIterator<Alignment> broad.pda.seq.segmentation.GenericAlignmentDataModel.getChrReadIterator

(

String

chromosome

)

throws IOException

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int broad.pda.seq.segmentation.GenericAlignmentDataModel.getChunkEnd

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

int broad.pda.seq.segmentation.GenericAlignmentDataModel.getChunkStart

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCounts

(

String

chr

)

throws IOException

Counts the number of reads for the specified chromosome

Returns

Exceptions

IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsOfUniqueOverlappers	(	Annotation	target,
		Annotation	exclude,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsOfUniqueOverlappers	(	Annotation	target,
		Gene	exclude,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsOnBase	(	String	chr,
		int	index
	)		throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsOnWindow	(	String	chr,
		int	startIndex,
		int	endIndex
	)		throws IOException

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double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsPerAlignment	(	Annotation	align,
		int	EF
	)		throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsPerAlignment

(

Annotation

align

)

throws IOException

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double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsPerAlignment	(	Annotation	align,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsPerAlignment	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsPerAlignment	(	Annotation[]	Annotation,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsPerAlignment	(	Annotation[]	Annotation,
		int	EF
	)		throws IOException

Similar to

See also

getCountsPerAlignment(Annotation[] Annotation, IntervalTree<Alignment> tree, int EF) but delegates the management of the alignment interval tree to the implementing class rather than the caller

Parameters

Annotation
EF

Returns

Exceptions

IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsPerAlignment	(	Annotation	align,
		Map< String, IntervalTree< Annotation >>	goodExonTree,
		IntervalTree< Alignment >	tree,
		int	extensionFactor
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsPerAlignmentForPolyA	(	Annotation	align,
		int	EF
	)		throws IOException

double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsPerAlignmentFullyContained	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsPerAlignmentUncached	(	String	chr,
		int	startIndex,
		int	endIndex
	)		throws IOException

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double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsPerAlignmentWithSameEndpointForPolyA	(	Annotation	align,
		int	EF,
		boolean	polyAIsOnRight,
		int	typicalOriginalAlignmentLength,
		int	maxDistanceFromOriginalAlignmentEndpoint
	)		throws IOException

double broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsPerAnnotationtranded	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		int	EF,
		String	orientation
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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int broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsWithinExons	(	Annotation	align,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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int broad.pda.seq.segmentation.GenericAlignmentDataModel.getCountsWithinExons	(	Annotation	align,
		Iterator< Alignment >	iter,
		int	EF
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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Iterator<Annotation> broad.pda.seq.segmentation.GenericAlignmentDataModel.getExonAnnotationOverlappingRegion

(

Annotation

align

)

throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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Iterator<Annotation> broad.pda.seq.segmentation.GenericAlignmentDataModel.getExonAnnotationOverlappingRegion

(

IntervalTree< Alignment >

tree

)

IntervalTree<Annotation> broad.pda.seq.segmentation.GenericAlignmentDataModel.getFullIntervalTreeAsAnnotation

(

String

chr

)

throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

GeneCounts broad.pda.seq.segmentation.GenericAlignmentDataModel.getGeneCounts	(	Gene	gene,
		int	extensionFactor
	)		throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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IntervalTree<Alignment> broad.pda.seq.segmentation.GenericAlignmentDataModel.getIntervalTree	(	String	chr,
		int	start,
		int	end
	)		throws IOException

public IntervalTree<Alignment> getIntervalTree(String chr, int start, int end){ System.err.print("Building tree from "+chr+" "+start+"-"+end + " - " ); int counter=0; IntervalTree<Alignment> tree=new IntervalTree<Alignment>(); CloseableIterator<Alignment> iter=getAnnotationOverlappingRegion(new Alignments(chr, start, end)); while(iter.hasNext()){ Alignment record=iter.next(); Annotation t1=new Alignments(record.getChr(), record.getAnnotationtart(), record.getAlignmentEnd()); Annotation t2=new Alignments(chr, start, end); if(t1.overlaps(t2)){ System.err.println("Getting interval overlappers "+start+"-"+end+" "+record.getChr()+":"+record.getAnnotationtart()+"-"+record.getAlignmentEnd());

            Node<Alignment> node=tree.find(record.getAnnotationtart(), record.getAlignmentEnd()+1);
            if(record.getMappingQuality()>1){
                if(node!=null){node.incrementCount();}
                else{tree.put(record.getAnnotationtart(), record.getAlignmentEnd()+1, record);}
                counter++;
            }
        }

else{System.err.println("WARN: Doesnt overlap queried: "+chr+":"+start+"-"+end+" got "+record.getChr()+":"+record.getAnnotationtart()+"-"+record.getAlignmentEnd());} } iter.close(); System.err.println(tree.size()+" "+counter); return tree; }

Exceptions

IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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IntervalTree<Alignment> broad.pda.seq.segmentation.GenericAlignmentDataModel.getIntervalTreeCached	(	String	chr,
		int	start,
		int	end
	)		throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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IntervalTree<Alignment> broad.pda.seq.segmentation.GenericAlignmentDataModel.getIntervalTreeTruncated	(	String	chr,
		int	start,
		int	end
	)		throws IOException

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IntervalTree<Alignment> broad.pda.seq.segmentation.GenericAlignmentDataModel.getIntervalTreeTruncatedCached	(	String	chromosome,
		int	start,
		int	end
	)		throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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double broad.pda.seq.segmentation.GenericAlignmentDataModel.getMinimumMappingQuality

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

String broad.pda.seq.segmentation.GenericAlignmentDataModel.getModelFilePath

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

double broad.pda.seq.segmentation.GenericAlignmentDataModel.getNumberOfSplicedReads

(

Annotation

align

)

throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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double broad.pda.seq.segmentation.GenericAlignmentDataModel.getNumberOfSplicedReads

(

)

Collection<Annotation> broad.pda.seq.segmentation.GenericAlignmentDataModel.getOverlappingRegions

(

String

chr

)

throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

Gene broad.pda.seq.segmentation.GenericAlignmentDataModel.getPeak	(	Gene	gene,
		Gene	startCodon,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

CloseableIterator<Alignment> broad.pda.seq.segmentation.GenericAlignmentDataModel.getReadIterator

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

CloseableIterator<Alignment> broad.pda.seq.segmentation.GenericAlignmentDataModel.getReadIterator

(

Annotation

region

)

throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

SAMFileHeader broad.pda.seq.segmentation.GenericAlignmentDataModel.getSamHeader

(

)

throws IOException

double broad.pda.seq.segmentation.GenericAlignmentDataModel.getScorePerAlignmentFromCache	(	Gene	window,
		IntervalTree< Alignment >	chunkAlignmentTree,
		int	extensionFactor
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

Collection<Annotation> broad.pda.seq.segmentation.GenericAlignmentDataModel.getSplicedReadExons

(

String

chr

)

throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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Map<Annotation, Integer> broad.pda.seq.segmentation.GenericAlignmentDataModel.getSplicedReads

(

Annotation

align

)

throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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Map<Annotation, Integer> broad.pda.seq.segmentation.GenericAlignmentDataModel.getSplicedReads	(	Annotation	align,
		final int	minIntronSize,
		final int	maxIntronSize,
		int	minNumIntrons,
		Sequence	chrSeq
	)		throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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Map<Annotation, Integer> broad.pda.seq.segmentation.GenericAlignmentDataModel.getSplicedReads	(	Annotation	align,
		final int	minIntronSize,
		final int	maxIntronSize
	)		throws IOException

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Map<Annotation, Integer> broad.pda.seq.segmentation.GenericAlignmentDataModel.getSplicedReads	(	Annotation	region,
		Predicate< Annotation >	filter
	)		throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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Map<Annotation, Integer> broad.pda.seq.segmentation.GenericAlignmentDataModel.getSplicedReads	(	Annotation	region,
		Collection< Predicate< Annotation >>	filters,
		int	minNumIntrons
	)		throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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Map<Annotation, Integer> broad.pda.seq.segmentation.GenericAlignmentDataModel.getSplicedReads	(	Annotation	region,
		Collection< Predicate< Annotation >>	filters,
		int	minNumIntrons,
		Sequence	chrSeq
	)		throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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Map<Annotation, Integer> broad.pda.seq.segmentation.GenericAlignmentDataModel.getSplicedReads	(	Annotation	region,
		Collection< Predicate< Annotation >>	filters
	)		throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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Map<Annotation, Integer> broad.pda.seq.segmentation.GenericAlignmentDataModel.getSplicedReads	(	Annotation	region,
		Collection< Predicate< Annotation >>	filters,
		Sequence	chrSeq
	)		throws IOException

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Map<Annotation, Integer> broad.pda.seq.segmentation.GenericAlignmentDataModel.getSplicedReads	(	int	minIntronSize,
		int	maxIntronSize
	)		throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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double broad.pda.seq.segmentation.GenericAlignmentDataModel.getSpliceWeightFactor

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

double [] broad.pda.seq.segmentation.GenericAlignmentDataModel.getTotalNumberOfMappedReads

(

)

double [] broad.pda.seq.segmentation.GenericAlignmentDataModel.getTotalNumberOfMappedStrandedReads

(

)

double broad.pda.seq.segmentation.GenericAlignmentDataModel.getTotalNumberOfReads

(

)

double broad.pda.seq.segmentation.GenericAlignmentDataModel.getTotalNumberOfStrandedReads

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

double broad.pda.seq.segmentation.GenericAlignmentDataModel.getWeight

(

)

throws IOException

boolean broad.pda.seq.segmentation.GenericAlignmentDataModel.hasNextExon

(

String

chr

)

throws IOException

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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boolean broad.pda.seq.segmentation.GenericAlignmentDataModel.isNegativeStranded

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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boolean broad.pda.seq.segmentation.GenericAlignmentDataModel.isPositiveStranded

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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boolean broad.pda.seq.segmentation.GenericAlignmentDataModel.isStranded

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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boolean broad.pda.seq.segmentation.GenericAlignmentDataModel.loadedPairsAsFragments

(

)

boolean broad.pda.seq.segmentation.GenericAlignmentDataModel.passes	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		int	EF,
		double	cutoff
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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long broad.pda.seq.segmentation.GenericAlignmentDataModel.passesCutoff	(	Annotation	align,
		IntervalTree< Alignment >	tree,
		int	EF,
		double	threshold
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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void broad.pda.seq.segmentation.GenericAlignmentDataModel.resetTreeCache

(

String

chr

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

void broad.pda.seq.segmentation.GenericAlignmentDataModel.resetTreeCache

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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void broad.pda.seq.segmentation.GenericAlignmentDataModel.restartIterator

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

void broad.pda.seq.segmentation.GenericAlignmentDataModel.setChunkSize

(

int

chunkSize

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

void broad.pda.seq.segmentation.GenericAlignmentDataModel.setExtensionFactor

(

int

extensionFactor

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

void broad.pda.seq.segmentation.GenericAlignmentDataModel.setFirstRead

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

void broad.pda.seq.segmentation.GenericAlignmentDataModel.setMinimumMappingQuality

(

double

minimumMappingQual

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

void broad.pda.seq.segmentation.GenericAlignmentDataModel.setNegativeStranded

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

void broad.pda.seq.segmentation.GenericAlignmentDataModel.setNormalizationStrategy

(

ReadCountNormalizer

normalizer

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

void broad.pda.seq.segmentation.GenericAlignmentDataModel.setPositiveStranded

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

void broad.pda.seq.segmentation.GenericAlignmentDataModel.setRemoveDuplicatesFlag

(

boolean

flag

)

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void broad.pda.seq.segmentation.GenericAlignmentDataModel.setSecondRead

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

void broad.pda.seq.segmentation.GenericAlignmentDataModel.setWeighReadCountsFlag

(

boolean

flag

)

Author

: skadri This function will set the weighReadCounts flag which decides how the reads are counted for each alignment

Parameters

flag	true if the read counts should be weighed by the value of the NH flag

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void broad.pda.seq.segmentation.GenericAlignmentDataModel.unsetStranded

(

)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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Gene broad.pda.seq.segmentation.GenericAlignmentDataModel.updateGeneByFirstCounts	(	Gene	gene,
		IntervalTree< Alignment >	tree,
		int	EF
	)

Implements broad.pda.seq.segmentation.AlignmentDataModel.

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

• java/broad/pda/seq/segmentation/GenericAlignmentDataModel.java