Package htsjdk.samtools

Interface BAMIndex

All Superinterfaces:

AutoCloseable, Closeable

All Known Subinterfaces:

BrowseableBAMIndex

All Known Implementing Classes:

AbstractBAMFileIndex, CSIIndex, DiskBasedBAMFileIndex, SRAIndex

public interface BAMIndex
extends Closeable

A basic interface for querying BAM indices.

Field Summary

Fields

Modifier and Type	Field	Description
static final String	BAI_INDEX_SUFFIX	Deprecated. since June 2019 Use FileExtensions.BAI_INDEX instead.
static final String	BAMIndexSuffix	Deprecated. since June 2019 Use FileExtensions.BAI_INDEX instead.
static final String	CSI_INDEX_SUFFIX	Deprecated. since June 2019 Use FileExtensions.CSI instead.

Method Summary

Modifier and Type	Method	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 Details

BAMIndexSuffix

@Deprecated
static final String BAMIndexSuffix

Deprecated.

since June 2019 Use FileExtensions.BAI_INDEX instead.

See Also:

• Constant Field Values

BAI_INDEX_SUFFIX

@Deprecated
static final String BAI_INDEX_SUFFIX

Deprecated.

since June 2019 Use FileExtensions.BAI_INDEX instead.

See Also:

• Constant Field Values

CSI_INDEX_SUFFIX

@Deprecated
static final String CSI_INDEX_SUFFIX

Deprecated.

since June 2019 Use FileExtensions.CSI instead.

See Also:

• Constant Field Values

Method Details

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 AutoCloseable

Specified by:

close in interface Closeable