htsjdk.samtools

Interface BrowseableBAMIndex

All Superinterfaces:

java.lang.AutoCloseable, BAMIndex, java.io.Closeable

All Known Implementing Classes:

SRAIndex

public interface BrowseableBAMIndex
extends BAMIndex

An index interface with additional functionality for querying and inspecting the structure of a BAM index.

Field Summary

Fields inherited from interface htsjdk.samtools.BAMIndex

BAMIndexSuffix

Method Summary

Modifier and Type	Method and Description
BinList	getBinsOverlapping(int referenceIndex, int startPos, int endPos) Get a list of bins in the BAM file that may contain SAMRecords for the given range.
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 size (number of bins in) a given level of a BAM index.
BAMFileSpan	getSpanOverlapping(Bin bin) Perform an overlapping query of all bins bounding the given location.

Methods inherited from interface htsjdk.samtools.BAMIndex

close, getMetaData, getSpanOverlapping, getStartOfLastLinearBin

Method Detail

getLevelSize

int getLevelSize(int levelNumber)

Gets the size (number of bins in) a given level of a BAM index.

Parameters:

levelNumber - Level for which to inspect the size.

Returns:

Size of the given level.

getLevelForBin

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

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

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.

getBinsOverlapping

BinList getBinsOverlapping(int referenceIndex,
                           int startPos,
                           int endPos)

Get a list of bins in the 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:

a list of bins that contain relevant data.

getSpanOverlapping

BAMFileSpan getSpanOverlapping(Bin bin)

Perform an overlapping query of all bins bounding the given location.

Parameters:

bin - The bin over which to perform an overlapping query.

Returns:

The file pointers