public class DiskBasedBAMFileIndex extends AbstractBAMFileIndex
BAMIndexSuffix
Constructor and Description |
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DiskBasedBAMFileIndex(java.io.File file,
SAMSequenceDictionary dictionary) |
DiskBasedBAMFileIndex(java.io.File file,
SAMSequenceDictionary dictionary,
boolean useMemoryMapping) |
DiskBasedBAMFileIndex(SeekableStream stream,
SAMSequenceDictionary dictionary) |
Modifier and Type | Method and Description |
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protected htsjdk.samtools.BAMIndexContent |
getQueryResults(int reference) |
BAMFileSpan |
getSpanOverlapping(int referenceIndex,
int startPos,
int endPos)
Get list of regions of BAM file that may contain SAMRecords for the given range
|
close, getFirstBinInLevel, getFirstLocusInBin, getLastLocusInBin, getLevelForBin, getLevelSize, getMaxAddressibleGenomicLocation, getMetaData, getNoCoordinateCount, getNumberOfReferences, getNumIndexLevels, getStartOfLastLinearBin, optimizeChunkList, query, regionToBins
public DiskBasedBAMFileIndex(java.io.File file, SAMSequenceDictionary dictionary)
public DiskBasedBAMFileIndex(SeekableStream stream, SAMSequenceDictionary dictionary)
public DiskBasedBAMFileIndex(java.io.File file, SAMSequenceDictionary dictionary, boolean useMemoryMapping)
public BAMFileSpan getSpanOverlapping(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, inclusiveprotected htsjdk.samtools.BAMIndexContent getQueryResults(int reference)
getQueryResults
in class AbstractBAMFileIndex