public abstract class AbstractBAMFileIndex extends java.lang.Object implements BAMIndex
BAI_INDEX_SUFFIX, BAMIndexSuffix, CSI_INDEX_SUFFIX
Modifier | Constructor and Description |
---|---|
protected |
AbstractBAMFileIndex(java.io.File file,
SAMSequenceDictionary dictionary) |
protected |
AbstractBAMFileIndex(java.io.File file,
SAMSequenceDictionary dictionary,
boolean useMemoryMapping) |
protected |
AbstractBAMFileIndex(htsjdk.samtools.IndexFileBuffer indexFileBuffer,
java.lang.String source,
SAMSequenceDictionary dictionary) |
protected |
AbstractBAMFileIndex(SeekableStream stream,
SAMSequenceDictionary dictionary) |
Modifier and Type | Method and Description |
---|---|
void |
close()
Close this index and release any associated resources.
|
protected SAMSequenceDictionary |
getBamDictionary() |
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 void |
initParameters()
Initialization method used for simplifying the constructor
hierarchy.
|
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 long |
position() |
protected htsjdk.samtools.BAMIndexContent |
query(int referenceSequence,
int startPos,
int endPos) |
protected void |
readBytes(byte[] bytes) |
protected void |
readChunks(int nChunks,
java.util.List<Chunk> chunks) |
protected int |
readInteger() |
protected long |
readLong() |
protected java.util.BitSet |
regionToBins(int startPos,
int endPos)
Deprecated.
Use
GenomicIndexUtil.regionToBins(int, int) instead.
Get candidate bins for the specified region |
protected void |
seek(long position) |
protected void |
setSequenceIndexes(int nReferences) |
protected void |
skipBytes(int count) |
protected void |
skipToSequence(int sequenceIndex) |
protected void |
verifyIndexMagicNumber(java.lang.String sourceName) |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
getSpanOverlapping
protected AbstractBAMFileIndex(SeekableStream stream, SAMSequenceDictionary dictionary)
protected AbstractBAMFileIndex(java.io.File file, SAMSequenceDictionary dictionary)
protected AbstractBAMFileIndex(java.io.File file, SAMSequenceDictionary dictionary, boolean useMemoryMapping)
protected AbstractBAMFileIndex(htsjdk.samtools.IndexFileBuffer indexFileBuffer, java.lang.String source, SAMSequenceDictionary dictionary)
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 BAMIndex
public BAMIndexMetaData getMetaData(int reference)
getMetaData
in interface BAMIndex
reference
- 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()
@Deprecated protected java.util.BitSet regionToBins(int startPos, int endPos)
GenomicIndexUtil.regionToBins(int, int)
instead.
Get candidate bins for the specified regionstartPos
- 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.protected void verifyIndexMagicNumber(java.lang.String sourceName)
protected void initParameters()
protected void readChunks(int nChunks, java.util.List<Chunk> chunks)
protected void skipToSequence(int sequenceIndex)
protected final void readBytes(byte[] bytes)
protected final int readInteger()
protected final long readLong()
protected final void skipBytes(int count)
protected final void seek(long position)
protected final long position()
protected final SAMSequenceDictionary getBamDictionary()
protected final void setSequenceIndexes(int nReferences)