Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.sra |
Modifier and Type | Method and Description |
---|---|
Chunk |
Chunk.clone() |
Chunk |
BinningIndexBuilder.FeatureToBeIndexed.getChunk() |
Chunk |
Bin.getLastChunk()
Warning: Currently only valid during index building, not when reading existing index,
(AbstractBAMFileIndex.optimizeChunkList doesn't maintain this)
|
protected Chunk |
BAMFileSpan.getSingleChunk()
Checks that there is only a single chunk for this span and returns it.
|
Modifier and Type | Method and Description |
---|---|
java.util.List<Chunk> |
BinningIndexContent.getAllChunks() |
java.util.List<Chunk> |
Bin.getChunkList()
Gets the list of chunks associated with this bin.
|
java.util.List<Chunk> |
BAMFileSpan.getChunks()
Gets the constituent chunks stored in this span.
|
java.util.List<Chunk> |
BinningIndexContent.getChunksOverlapping(int startPos,
int endPos) |
static java.util.List<Chunk> |
Chunk.optimizeChunkList(java.util.List<Chunk> chunks,
long minimumOffset) |
protected java.util.List<Chunk> |
AbstractBAMFileIndex.optimizeChunkList(java.util.List<Chunk> chunks,
long minimumOffset)
Deprecated.
Invoke htsjdk.samtools.Chunk#optimizeChunkList(java.util.List
|
Modifier and Type | Method and Description |
---|---|
protected void |
BAMFileSpan.add(Chunk chunk)
Adds a new chunk to this list.
|
void |
Bin.addInitialChunk(Chunk newChunk)
Adds the first chunk to the bin
|
int |
Chunk.compareTo(Chunk chunk) |
boolean |
Chunk.isAdjacentTo(Chunk other)
Returns whether two chunks overlap.
|
boolean |
Chunk.overlaps(Chunk other)
Returns whether two chunks overlap.
|
void |
Bin.setLastChunk(Chunk c)
Optimization to keep lastChunk instead of iterating over all chunks repeatedly
|
Modifier and Type | Method and Description |
---|---|
static java.util.List<Chunk> |
Chunk.optimizeChunkList(java.util.List<Chunk> chunks,
long minimumOffset) |
protected java.util.List<Chunk> |
AbstractBAMFileIndex.optimizeChunkList(java.util.List<Chunk> chunks,
long minimumOffset)
Deprecated.
Invoke htsjdk.samtools.Chunk#optimizeChunkList(java.util.List
|
void |
Bin.setChunkList(java.util.List<Chunk> list)
Sets the chunks associated with this bin
|
Constructor and Description |
---|
BAMFileSpan(Chunk chunk)
Convenience constructor to construct a BAM file span from
a single chunk.
|
Constructor and Description |
---|
BAMFileSpan(java.util.List<Chunk> chunks)
Create a new chunk list from the given list of chunks.
|
SRAIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
ReferenceCache cachedReferences,
SRAIterator.RecordRangeInfo recordRangeInfo,
java.util.List<Chunk> chunks) |
Constructor and Description |
---|
SRAAlignmentIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
ReferenceCache cachedReferences,
SRAIterator.RecordRangeInfo recordRangeInfo,
Chunk chunk) |
SRAUnalignmentIterator(SRAAccession accession,
ngs.ReadCollection run,
SAMFileHeader header,
SRAIterator.RecordRangeInfo recordRangeInfo,
Chunk chunk) |