java.lang.Object
- htsjdk.samtools.AbstractBAMFileIndex
- - htsjdk.samtools.CSIIndex

All Implemented Interfaces:

BAMIndex, BrowseableBAMIndex, Closeable, 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	Description
`CSIIndex(SeekableStream stream, SAMSequenceDictionary dictionary)`	Constructors
`CSIIndex(File file, boolean enableMemoryMapping, SAMSequenceDictionary dictionary)`
`CSIIndex(Path path, SAMSequenceDictionary dictionary)`

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	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
`Long`	`getNoCoordinateCount()`	Returns count of records unassociated with any reference.
`int`	`getNumberOfReferences()`
`int`	`getParentBinNumber(int binNumber)`
`int`	`getParentBinNumber(Bin bin)`
`htsjdk.samtools.BAMIndexContent`	`getQueryResults(int referenceSequence)`
`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.
`BAMFileSpan`	`getSpanOverlapping(Bin bin)`	Perform an overlapping query of all bins bounding the given location.
`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(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(Path path,
                SAMSequenceDictionary dictionary)
         throws IOException
```
    Throws:
    
    IOException
  - CSIIndex
```
public CSIIndex(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(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 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

Class CSIIndex

Field Summary

Fields inherited from interface htsjdk.samtools.BAMIndex

Constructor Summary

Method Summary

Methods inherited from class htsjdk.samtools.AbstractBAMFileIndex

Methods inherited from class java.lang.Object

Methods inherited from interface htsjdk.samtools.BAMIndex

Constructor Detail

CSIIndex

CSIIndex

CSIIndex

Method Detail

getBinDepth

getMinShift

getMaxBins

getMaxSpan

getAuxData

getNumberOfReferences

getLevelSize

getFirstBinInLevelForCSI

getLevelForBin

getFirstLocusInBin

getLastLocusInBin

getBinsOverlapping

getSpanOverlapping

getSpanOverlapping

getStartOfLastLinearBin

verifyIndexMagicNumber

initParameters

getParentBinNumber

getParentBinNumber

query

getMetaData

getNoCoordinateCount

getQueryResults

skipToSequence