Package htsjdk.samtools

Class DiskBasedBAMFileIndex

java.lang.Object

htsjdk.samtools.AbstractBAMFileIndex

htsjdk.samtools.DiskBasedBAMFileIndex

All Implemented Interfaces:

BAMIndex, Closeable, AutoCloseable

public class DiskBasedBAMFileIndex
extends AbstractBAMFileIndex

A class for reading BAM file indices, hitting the disk once per query.

Field Summary

Fields inherited from interface htsjdk.samtools.BAMIndex

BAI_INDEX_SUFFIX, BAMIndexSuffix, CSI_INDEX_SUFFIX

Constructor Summary

Constructors

Constructor	Description
DiskBasedBAMFileIndex(SeekableStream stream, SAMSequenceDictionary dictionary)
DiskBasedBAMFileIndex(File file, SAMSequenceDictionary dictionary)
DiskBasedBAMFileIndex(File file, SAMSequenceDictionary dictionary, boolean useMemoryMapping)

Method Summary

Modifier and Type	Method	Description
protected htsjdk.samtools.BAMIndexContent	getQueryResults(int reference)
BAMFileSpan	getSpanOverlapping(int referenceIndex, int startPos, int endPos)	Get list of regions of BAM file that may contain SAMRecords for the given range

Methods inherited from class htsjdk.samtools.AbstractBAMFileIndex

close, getBamDictionary, getFirstBinInLevel, getFirstLocusInBin, getLastLocusInBin, getLevelForBin, getLevelSize, getMaxAddressibleGenomicLocation, getMetaData, getNoCoordinateCount, getNumberOfReferences, getNumIndexLevels, getStartOfLastLinearBin, initParameters, optimizeChunkList, position, query, readBytes, readChunks, readInteger, readLong, regionToBins, seek, setSequenceIndexes, skipBytes, skipToSequence, verifyIndexMagicNumber

Methods inherited from class java.lang.Object

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

Constructor Details

DiskBasedBAMFileIndex

public DiskBasedBAMFileIndex(File file,
 SAMSequenceDictionary dictionary)

DiskBasedBAMFileIndex

public DiskBasedBAMFileIndex(SeekableStream stream,
 SAMSequenceDictionary dictionary)

DiskBasedBAMFileIndex

public DiskBasedBAMFileIndex(File file,
 SAMSequenceDictionary dictionary,
 boolean useMemoryMapping)

Method Details

getSpanOverlapping

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

Get list of regions of BAM file that may contain SAMRecords for the given range

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:

array of pairs of virtual file positions. Each pair is the first and last virtual file position in a range that can be scanned to find SAMRecords that overlap the given positions. The last position in each pair is a virtual file pointer to the first SAMRecord beyond the range that may contain the indicated SAMRecords.

getQueryResults

protected htsjdk.samtools.BAMIndexContent getQueryResults(int reference)

Specified by:

getQueryResults in class AbstractBAMFileIndex