htsjdk.samtools

Class CSIIndex

java.lang.Object

htsjdk.samtools.AbstractBAMFileIndex

htsjdk.samtools.CSIIndex

All Implemented Interfaces:

BAMIndex, BrowseableBAMIndex, java.io.Closeable, java.lang.AutoCloseable

public class CSIIndex
extends AbstractBAMFileIndex
implements BrowseableBAMIndex

Implementation of the CSI index for BAM files. The CSI index extends the BAI index by allowing a more flexible binning scheme, with variable depth (number of levels) and bin sizes, thus allowing for genomic regions longer than 2^29-1.

Field Summary

Fields inherited from interface htsjdk.samtools.BAMIndex

BAI_INDEX_SUFFIX, BAMIndexSuffix, CSI_INDEX_SUFFIX

Constructor Summary

Constructors

Constructor and Description
CSIIndex(java.io.File file, boolean enableMemoryMapping, SAMSequenceDictionary dictionary)
CSIIndex(java.nio.file.Path path, SAMSequenceDictionary dictionary)
CSIIndex(SeekableStream stream, SAMSequenceDictionary dictionary) Constructors

Method Summary

Modifier and Type	Method and Description
byte[]	getAuxData()
int	getBinDepth() Bin depth is the number of levels of the index.
BinList	getBinsOverlapping(int referenceIndex, int startPos, int endPos) Get a list of bins in the BAM file that may contain SAMRecords for the given range.
int	getFirstBinInLevelForCSI(int levelNumber) Extends the functionality of AbstractBAMFileIndex.getFirstBinInLevel(int) , which cannot be overridden due to its static nature.
int	getFirstLocusInBin(Bin bin) Gets the first locus that this bin can index into.
int	getLastLocusInBin(Bin bin) Gets the last locus that this bin can index into.
int	getLevelForBin(Bin bin) Gets the level associated with the given bin number.
int	getLevelSize(int levelNumber) Computes the number of bins on the given level.
int	getMaxBins()
int	getMaxSpan()
BAMIndexMetaData	getMetaData(int reference) Return meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
int	getMinShift() 2^(min shift) is the smallest width of a bin
java.lang.Long	getNoCoordinateCount() Returns count of records unassociated with any reference.
int	getNumberOfReferences()
int	getParentBinNumber(Bin bin)
int	getParentBinNumber(int binNumber)
htsjdk.samtools.BAMIndexContent	getQueryResults(int referenceSequence)
BAMFileSpan	getSpanOverlapping(Bin bin) Perform an overlapping query of all bins bounding the given location.
BAMFileSpan	getSpanOverlapping(int referenceIndex, int startPos, int endPos) Gets the compressed chunks which should be searched for the contents of records contained by the span referenceIndex:startPos-endPos, inclusive.
long	getStartOfLastLinearBin() Use to get close to the unmapped reads at the end of a BAM file.
protected void	initParameters() Initialization method used for simplifying the constructor hierarchy.
protected htsjdk.samtools.BAMIndexContent	query(int referenceSequence, int startPos, int endPos)
protected void	skipToSequence(int sequenceIndex)
protected void	verifyIndexMagicNumber(java.lang.String sourceName)

Methods inherited from class htsjdk.samtools.AbstractBAMFileIndex

close, getBamDictionary, getFirstBinInLevel, getMaxAddressibleGenomicLocation, getNumIndexLevels, optimizeChunkList, position, readBytes, readChunks, readInteger, readLong, regionToBins, seek, setSequenceIndexes, skipBytes

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface htsjdk.samtools.BAMIndex

close

Constructor Detail

CSIIndex

public CSIIndex(SeekableStream stream,
                SAMSequenceDictionary dictionary)

Constructors

CSIIndex

public CSIIndex(java.nio.file.Path path,
                SAMSequenceDictionary dictionary)
         throws java.io.IOException

Throws:

java.io.IOException

CSIIndex

public CSIIndex(java.io.File file,
                boolean enableMemoryMapping,
                SAMSequenceDictionary dictionary)

Method Detail

getBinDepth

public int getBinDepth()

Bin depth is the number of levels of the index. By default, BAI has 6 levels. CSI makes this variable.

getMinShift

public int getMinShift()

2^(min shift) is the smallest width of a bin

getMaxBins

public int getMaxBins()

getMaxSpan

public int getMaxSpan()

getAuxData

public byte[] getAuxData()

getNumberOfReferences

public int getNumberOfReferences()

Overrides:

getNumberOfReferences in class AbstractBAMFileIndex

getLevelSize

public int getLevelSize(int levelNumber)

Computes the number of bins on the given level.

Specified by:

getLevelSize in interface BrowseableBAMIndex

Overrides:

getLevelSize in class AbstractBAMFileIndex

Parameters:

levelNumber - Level for which to compute the size.

Returns:

getFirstBinInLevelForCSI

public int getFirstBinInLevelForCSI(int levelNumber)

Extends the functionality of AbstractBAMFileIndex.getFirstBinInLevel(int) , which cannot be overridden due to its static nature.

getLevelForBin

public int getLevelForBin(Bin bin)

Description copied from class: AbstractBAMFileIndex

Gets the level associated with the given bin number.

Specified by:

getLevelForBin in interface BrowseableBAMIndex

Overrides:

getLevelForBin in class AbstractBAMFileIndex

Parameters:

bin - The bin for which to determine the level.

Returns:

the level associated with the given bin number.

getFirstLocusInBin

public int getFirstLocusInBin(Bin bin)

Description copied from class: AbstractBAMFileIndex

Gets the first locus that this bin can index into.

Specified by:

getFirstLocusInBin in interface BrowseableBAMIndex

Overrides:

getFirstLocusInBin in class AbstractBAMFileIndex

Parameters:

bin - The bin to test.

Returns:

The last position that the given bin can represent.

getLastLocusInBin

public int getLastLocusInBin(Bin bin)

Description copied from class: AbstractBAMFileIndex

Gets the last locus that this bin can index into.

Specified by:

getLastLocusInBin in interface BrowseableBAMIndex

Overrides:

getLastLocusInBin in class AbstractBAMFileIndex

Parameters:

bin - The bin to test.

Returns:

The last position that the given bin can represent.

getBinsOverlapping

public BinList getBinsOverlapping(int referenceIndex,
                                  int startPos,
                                  int endPos)

Description copied from interface: BrowseableBAMIndex

Get a list of bins in the BAM file that may contain SAMRecords for the given range.

Specified by:

getBinsOverlapping in interface BrowseableBAMIndex

Parameters:

referenceIndex - sequence of desired SAMRecords

startPos - 1-based start of the desired interval, inclusive

endPos - 1-based end of the desired interval, inclusive

Returns:

a list of bins that contain relevant data.

getSpanOverlapping

public BAMFileSpan getSpanOverlapping(int referenceIndex,
                                      int startPos,
                                      int endPos)

Description copied from interface: BAMIndex

Gets the compressed chunks which should be searched for the contents of records contained by the span referenceIndex:startPos-endPos, inclusive. See the BAM spec for more information on how a chunk is represented.

Specified by:

getSpanOverlapping in interface BAMIndex

Parameters:

referenceIndex - The contig.

startPos - Genomic start of query.

endPos - Genomic end of query.

Returns:

A file span listing the chunks in the BAM file.

getSpanOverlapping

public BAMFileSpan getSpanOverlapping(Bin bin)

Description copied from interface: BrowseableBAMIndex

Perform an overlapping query of all bins bounding the given location.

Specified by:

getSpanOverlapping in interface BrowseableBAMIndex

Parameters:

bin - The bin over which to perform an overlapping query.

Returns:

The file pointers

getStartOfLastLinearBin

public long getStartOfLastLinearBin()

Description copied from class: AbstractBAMFileIndex

Use to get close to the unmapped reads at the end of a BAM file.

Specified by:

getStartOfLastLinearBin in interface BAMIndex

Overrides:

getStartOfLastLinearBin in class AbstractBAMFileIndex

Returns:

The file offset of the first record in the last linear bin, or -1 if there are no elements in linear bins (i.e. no mapped reads).

verifyIndexMagicNumber

protected void verifyIndexMagicNumber(java.lang.String sourceName)

Overrides:

verifyIndexMagicNumber in class AbstractBAMFileIndex

initParameters

protected final void initParameters()

Description copied from class: AbstractBAMFileIndex

Initialization method used for simplifying the constructor hierarchy.

Overrides:

initParameters in class AbstractBAMFileIndex

getParentBinNumber

public int getParentBinNumber(int binNumber)

getParentBinNumber

public int getParentBinNumber(Bin bin)

query

protected htsjdk.samtools.BAMIndexContent query(int referenceSequence,
                                                int startPos,
                                                int endPos)

Overrides:

query in class AbstractBAMFileIndex

getMetaData

public BAMIndexMetaData getMetaData(int reference)

Return meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records

Specified by:

getMetaData in interface BAMIndex

Overrides:

getMetaData in class AbstractBAMFileIndex

Parameters:

reference - the reference of interest

Returns:

meta data for the reference

getNoCoordinateCount

public java.lang.Long getNoCoordinateCount()

Returns count of records unassociated with any reference. Call before the index file is closed

Overrides:

getNoCoordinateCount in class AbstractBAMFileIndex

Returns:

meta data at the end of the bam index that indicates count of records holding no coordinates or null if no meta data (old index format)

getQueryResults

public htsjdk.samtools.BAMIndexContent getQueryResults(int referenceSequence)

Specified by:

getQueryResults in class AbstractBAMFileIndex

skipToSequence

protected void skipToSequence(int sequenceIndex)

Overrides:

skipToSequence in class AbstractBAMFileIndex