htsjdk.samtools

Class LinearBAMIndex

java.lang.Object

htsjdk.samtools.AbstractBAMFileIndex

htsjdk.samtools.LinearBAMIndex

All Implemented Interfaces:

htsjdk.samtools.BAMIndex, htsjdk.samtools.BrowseableBAMIndex, Closeable, AutoCloseable

public class LinearBAMIndex
extends htsjdk.samtools.AbstractBAMFileIndex

The htsjdk APIs for accessing the linear BAM index are private...

Field Summary

Fields inherited from interface htsjdk.samtools.BAMIndex

BAMIndexSuffix

Constructor Summary

Constructors

Constructor and Description
LinearBAMIndex(htsjdk.samtools.seekablestream.SeekableStream stream, htsjdk.samtools.SAMSequenceDictionary dict)

Method Summary

Modifier and Type	Method and Description
htsjdk.samtools.BinList	getBinsOverlapping(int arg0, int arg1, int arg2)
htsjdk.samtools.LinearIndex	getLinearIndex(int idx)
protected htsjdk.samtools.BAMIndexContent	getQueryResults(int arg0)
htsjdk.samtools.BAMFileSpan	getSpanOverlapping(htsjdk.samtools.Bin arg0)
htsjdk.samtools.BAMFileSpan	getSpanOverlapping(int arg0, int arg1, int arg2)

Methods inherited from class htsjdk.samtools.AbstractBAMFileIndex

close, getFirstBinInLevel, getFirstLocusInBin, getLastLocusInBin, getLevelForBin, getLevelSize, getMaxAddressibleGenomicLocation, getMetaData, getNoCoordinateCount, getNumberOfReferences, getNumIndexLevels, getStartOfLastLinearBin, optimizeChunkList, query, regionToBins

Methods inherited from class java.lang.Object

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

Methods inherited from interface htsjdk.samtools.BrowseableBAMIndex

getFirstLocusInBin, getLastLocusInBin, getLevelForBin, getLevelSize

Methods inherited from interface htsjdk.samtools.BAMIndex

close, getMetaData, getStartOfLastLinearBin

Constructor Detail

LinearBAMIndex

public LinearBAMIndex(htsjdk.samtools.seekablestream.SeekableStream stream,
                      htsjdk.samtools.SAMSequenceDictionary dict)

Method Detail

getLinearIndex

public htsjdk.samtools.LinearIndex getLinearIndex(int idx)

getSpanOverlapping

public htsjdk.samtools.BAMFileSpan getSpanOverlapping(int arg0,
                                                      int arg1,
                                                      int arg2)

Specified by:

getSpanOverlapping in interface htsjdk.samtools.BAMIndex

getBinsOverlapping

public htsjdk.samtools.BinList getBinsOverlapping(int arg0,
                                                  int arg1,
                                                  int arg2)

Specified by:

getBinsOverlapping in interface htsjdk.samtools.BrowseableBAMIndex

getSpanOverlapping

public htsjdk.samtools.BAMFileSpan getSpanOverlapping(htsjdk.samtools.Bin arg0)

Specified by:

getSpanOverlapping in interface htsjdk.samtools.BrowseableBAMIndex

getQueryResults

protected htsjdk.samtools.BAMIndexContent getQueryResults(int arg0)

Specified by:

getQueryResults in class htsjdk.samtools.AbstractBAMFileIndex