htsjdk.samtools

Interface BAMIndex

All Superinterfaces:

java.lang.AutoCloseable, java.io.Closeable

All Known Subinterfaces:

BrowseableBAMIndex

All Known Implementing Classes:

AbstractBAMFileIndex, DiskBasedBAMFileIndex, SRAIndex

public interface BAMIndex
extends java.io.Closeable

A basic interface for querying BAM indices.

Field Summary

Fields

Modifier and Type	Field and Description
static java.lang.String	BAMIndexSuffix

Method Summary

Modifier and Type	Method and Description
void	close() Close the index and release any associated resources.
BAMIndexMetaData	getMetaData(int reference) Gets meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
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.
long	getStartOfLastLinearBin() Gets the start of the last linear bin in the index.

Field Detail

BAMIndexSuffix

static final java.lang.String BAMIndexSuffix

See Also:

Constant Field Values

Method Detail

getSpanOverlapping

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. See the BAM spec for more information on how a chunk is represented.

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.

getStartOfLastLinearBin

long getStartOfLastLinearBin()

Gets the start of the last linear bin in the index.

Returns:

The chunk indicating the start of the last bin in the linear index.

getMetaData

BAMIndexMetaData getMetaData(int reference)

Gets meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records

Parameters:

reference - the reference of interest

Returns:

meta data for the reference

close

void close()

Close the index and release any associated resources.

Specified by:

close in interface java.lang.AutoCloseable

Specified by:

close in interface java.io.Closeable