BAMIndexSuffix
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.
|
htsjdk.samtools.BAMFileSpan |
getSpanOverlapping(Bin bin)
Perform an overlapping query of all bins bounding the given location.
|
close, getMetaData, getSpanOverlapping, getStartOfLastLinearBin
int getLevelSize(int levelNumber)
levelNumber
- Level for which to inspect the size.int getLevelForBin(Bin bin)
bin
- The bin for which to determine the level.int getFirstLocusInBin(Bin bin)
bin
- The bin to test.int getLastLocusInBin(Bin bin)
bin
- The bin to test.BinList getBinsOverlapping(int referenceIndex, int startPos, int endPos)
referenceIndex
- sequence of desired SAMRecordsstartPos
- 1-based start of the desired interval, inclusiveendPos
- 1-based end of the desired interval, inclusivehtsjdk.samtools.BAMFileSpan getSpanOverlapping(Bin bin)
bin
- The bin over which to perform an overlapping query.