AbstractBAMFileIndex (htsjdk 2.14.3 API)

java.lang.Object
- htsjdk.samtools.AbstractBAMFileIndex

All Implemented Interfaces:

BAMIndex, Closeable, AutoCloseable

Direct Known Subclasses:

DiskBasedBAMFileIndex
```
public abstract class AbstractBAMFileIndex
extends 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	Description
`protected`	`AbstractBAMFileIndex(SeekableStream stream, SAMSequenceDictionary dictionary)`
`protected`	`AbstractBAMFileIndex(File file, SAMSequenceDictionary dictionary)`
`protected`	`AbstractBAMFileIndex(File file, SAMSequenceDictionary dictionary, boolean useMemoryMapping)`

Method Summary

All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Deprecated Methods
Modifier and Type	Method	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
`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 List<Chunk>`	`optimizeChunkList(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 BitSet`	`regionToBins(int startPos, int endPos)`	Get candidate bins for the specified region

Methods inherited from interface htsjdk.samtools.BAMIndex
getSpanOverlapping

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - AbstractBAMFileIndex
```
protected AbstractBAMFileIndex(SeekableStream stream,
                               SAMSequenceDictionary dictionary)
```
  - AbstractBAMFileIndex
```
protected AbstractBAMFileIndex(File file,
                               SAMSequenceDictionary dictionary)
```
  - AbstractBAMFileIndex
```
protected AbstractBAMFileIndex(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 AutoCloseable
    
    Specified by:
    
    close in interface BAMIndex
    
    Specified by:
    
    close in interface Closeable
  - 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 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 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 List<Chunk> optimizeChunkList(List<Chunk> chunks,
                                        long minimumOffset)
```
    Deprecated.
    Invoke Chunk.optimizeChunkList(java.util.List<htsjdk.samtools.Chunk>, long) directly.

Class AbstractBAMFileIndex

Field Summary

Fields inherited from interface htsjdk.samtools.BAMIndex

Constructor Summary

Method Summary

Methods inherited from interface htsjdk.samtools.BAMIndex

Methods inherited from class java.lang.Object

Constructor Detail

AbstractBAMFileIndex

AbstractBAMFileIndex

AbstractBAMFileIndex

Method Detail

close

getNumIndexLevels

getFirstBinInLevel

getLevelSize

getLevelForBin

getFirstLocusInBin

getLastLocusInBin

getNumberOfReferences

getStartOfLastLinearBin

getMetaData

getNoCoordinateCount

query

getQueryResults

getMaxAddressibleGenomicLocation

regionToBins

optimizeChunkList