htsjdk.samtools

Class AbstractBAMFileIndex

java.lang.Object

htsjdk.samtools.AbstractBAMFileIndex

All Implemented Interfaces:

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

Direct Known Subclasses:

DiskBasedBAMFileIndex

public abstract class AbstractBAMFileIndex
extends java.lang.Object
implements BAMIndex

Provides basic, generic capabilities to be used reading BAM index files. Users can subclass this class to create new BAM index functionality for adding querying facilities, changing caching behavior, etc. Of particular note: the AbstractBAMFileIndex is, by design, the only class aware of the details of the BAM index file format (other than the four classes representing the data, BAMIndexContent, Bin, Chunk, LinearIndex, and the classes for building the BAM index). Anyone wanting to implement a reader for a differing or extended BAM index format should implement BAMIndex directly.

Field Summary

Fields inherited from interface htsjdk.samtools.BAMIndex

BAMIndexSuffix

Constructor Summary

Constructors

Modifier	Constructor and Description
protected	AbstractBAMFileIndex(java.io.File file, SAMSequenceDictionary dictionary)
protected	AbstractBAMFileIndex(java.io.File file, SAMSequenceDictionary dictionary, boolean useMemoryMapping)
protected	AbstractBAMFileIndex(SeekableStream stream, SAMSequenceDictionary dictionary)

Method Summary

Modifier and Type	Method and Description
void	close() Close this index and release any associated resources.
static int	getFirstBinInLevel(int levelNumber) Gets the first bin in the given level.
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) Gets the number of bins in the given level.
protected int	getMaxAddressibleGenomicLocation() Gets the possible number of bins for a given reference sequence.
BAMIndexMetaData	getMetaData(int reference) Return meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
java.lang.Long	getNoCoordinateCount() Returns count of records unassociated with any reference.
int	getNumberOfReferences()
static int	getNumIndexLevels() Get the number of levels employed by this index.
protected abstract htsjdk.samtools.BAMIndexContent	getQueryResults(int reference)
long	getStartOfLastLinearBin() Use to get close to the unmapped reads at the end of a BAM file.
protected java.util.List<Chunk>	optimizeChunkList(java.util.List<Chunk> chunks, long minimumOffset) Deprecated. Invoke Chunk.optimizeChunkList(java.util.List<htsjdk.samtools.Chunk>, long) directly.
protected htsjdk.samtools.BAMIndexContent	query(int referenceSequence, int startPos, int endPos)
protected java.util.BitSet	regionToBins(int startPos, int endPos) Get candidate bins for the specified region

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

getSpanOverlapping

Constructor Detail

AbstractBAMFileIndex

protected AbstractBAMFileIndex(SeekableStream stream,
                               SAMSequenceDictionary dictionary)

AbstractBAMFileIndex

protected AbstractBAMFileIndex(java.io.File file,
                               SAMSequenceDictionary dictionary)

AbstractBAMFileIndex

protected AbstractBAMFileIndex(java.io.File file,
                               SAMSequenceDictionary dictionary,
                               boolean useMemoryMapping)

Method Detail

close

public void close()

Close this index and release any associated resources.

Specified by:

close in interface BAMIndex

Specified by:

close in interface java.io.Closeable

Specified by:

close in interface java.lang.AutoCloseable

getNumIndexLevels

public static int getNumIndexLevels()

Get the number of levels employed by this index.

Returns:

Number of levels in this index.

getFirstBinInLevel

public static int getFirstBinInLevel(int levelNumber)

Gets the first bin in the given level.

Parameters:

levelNumber - Level number. 0-based.

Returns:

The first bin in this level.

getLevelSize

public int getLevelSize(int levelNumber)

Gets the number of bins in the given level.

Parameters:

levelNumber - Level number. 0-based.

Returns:

The size (number of possible bins) of the given level.

getLevelForBin

public int getLevelForBin(Bin bin)

Gets the level associated with the given bin number.

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)

Gets the first locus that this bin can index into.

Parameters:

bin - The bin to test.

Returns:

The last position that the given bin can represent.

getLastLocusInBin

public int getLastLocusInBin(Bin bin)

Gets the last locus that this bin can index into.

Parameters:

bin - The bin to test.

Returns:

The last position that the given bin can represent.

getNumberOfReferences

public int getNumberOfReferences()

getStartOfLastLinearBin

public long getStartOfLastLinearBin()

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

Specified by:

getStartOfLastLinearBin in interface BAMIndex

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).

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

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

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)

query

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

getQueryResults

protected abstract htsjdk.samtools.BAMIndexContent getQueryResults(int reference)

getMaxAddressibleGenomicLocation

protected int getMaxAddressibleGenomicLocation()

Gets the possible number of bins for a given reference sequence.

Returns:

How many bins could possibly be used according to this indexing scheme to index a single contig.

regionToBins

protected java.util.BitSet regionToBins(int startPos,
                                        int endPos)

Get candidate bins for the specified region

Parameters:

startPos - 1-based start of target region, inclusive.

endPos - 1-based end of target region, inclusive.

Returns:

bit set for each bin that may contain SAMRecords in the target region.

optimizeChunkList

@Deprecated
protected java.util.List<Chunk> optimizeChunkList(java.util.List<Chunk> chunks,
                                                              long minimumOffset)

Deprecated. Invoke Chunk.optimizeChunkList(java.util.List<htsjdk.samtools.Chunk>, long) directly.