public abstract class AbstractBAMFileIndex extends java.lang.Object implements BAMIndex
BAMIndexSuffix| Modifier | Constructor and Description |
|---|---|
protected |
AbstractBAMFileIndex(java.io.File file,
SAMSequenceDictionary dictionary) |
protected |
AbstractBAMFileIndex(java.io.File file,
SAMSequenceDictionary dictionary,
boolean useMemoryMapping) |
protected |
AbstractBAMFileIndex(SeekableStream stream,
SAMSequenceDictionary dictionary) |
| Modifier and Type | Method and Description |
|---|---|
void |
close()
Close this index and release any associated resources.
|
static int |
getFirstBinInLevel(int levelNumber)
Gets the first bin in the given level.
|
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 number of bins in the given level.
|
protected int |
getMaxAddressibleGenomicLocation()
Gets the possible number of bins for a given reference sequence.
|
BAMIndexMetaData |
getMetaData(int reference)
Return meta data for the given reference including information about number of aligned, unaligned, and noCoordinate records
|
java.lang.Long |
getNoCoordinateCount()
Returns count of records unassociated with any reference.
|
int |
getNumberOfReferences() |
static int |
getNumIndexLevels()
Get the number of levels employed by this index.
|
protected abstract htsjdk.samtools.BAMIndexContent |
getQueryResults(int reference) |
long |
getStartOfLastLinearBin()
Use to get close to the unmapped reads at the end of a BAM file.
|
protected java.util.List<Chunk> |
optimizeChunkList(java.util.List<Chunk> chunks,
long minimumOffset)
Deprecated.
Invoke
Chunk.optimizeChunkList(java.util.List<htsjdk.samtools.Chunk>, long) directly. |
protected htsjdk.samtools.BAMIndexContent |
query(int referenceSequence,
int startPos,
int endPos) |
protected java.util.BitSet |
regionToBins(int startPos,
int endPos)
Get candidate bins for the specified region
|
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, waitgetSpanOverlappingprotected AbstractBAMFileIndex(SeekableStream stream, SAMSequenceDictionary dictionary)
protected AbstractBAMFileIndex(java.io.File file,
SAMSequenceDictionary dictionary)
protected AbstractBAMFileIndex(java.io.File file,
SAMSequenceDictionary dictionary,
boolean useMemoryMapping)
public void close()
public static int getNumIndexLevels()
public static int getFirstBinInLevel(int levelNumber)
levelNumber - Level number. 0-based.public int getLevelSize(int levelNumber)
levelNumber - Level number. 0-based.public int getLevelForBin(Bin bin)
bin - The bin for which to determine the level.public int getFirstLocusInBin(Bin bin)
bin - The bin to test.public int getLastLocusInBin(Bin bin)
bin - The bin to test.public int getNumberOfReferences()
public long getStartOfLastLinearBin()
getStartOfLastLinearBin in interface BAMIndexpublic BAMIndexMetaData getMetaData(int reference)
getMetaData in interface BAMIndexreference - the reference of interestpublic java.lang.Long getNoCoordinateCount()
protected htsjdk.samtools.BAMIndexContent query(int referenceSequence,
int startPos,
int endPos)
protected abstract htsjdk.samtools.BAMIndexContent getQueryResults(int reference)
protected int getMaxAddressibleGenomicLocation()
protected java.util.BitSet regionToBins(int startPos,
int endPos)
startPos - 1-based start of target region, inclusive.endPos - 1-based end of target region, inclusive.@Deprecated protected java.util.List<Chunk> optimizeChunkList(java.util.List<Chunk> chunks, long minimumOffset)
Chunk.optimizeChunkList(java.util.List<htsjdk.samtools.Chunk>, long) directly.