Package | Description |
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htsjdk.samtools |
Modifier and Type | Class and Description |
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class |
BAMFileSpan
An ordered list of chunks, capable of representing a set of discontiguous
regions in the BAM file.
|
Modifier and Type | Method and Description |
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SAMFileSpan |
SAMFileSpan.getContentsFollowing()
Gets a pointer over the data immediately following this span.
|
SAMFileSpan |
BAMFileSpan.getContentsFollowing()
Gets a file span over the data immediately following this span.
|
SAMFileSpan |
SAMFileSource.getFilePointer()
A pointer to the region on disk from which the read originated.
|
SAMFileSpan |
CRAMFileReader.getFilePointerSpanningReads() |
SAMFileSpan |
SamReader.Indexing.getFilePointerSpanningReads()
Gets a pointer spanning all reads in the BAM file.
|
SAMFileSpan |
SamReader.PrimitiveSamReader.getFilePointerSpanningReads() |
SAMFileSpan |
SamReader.PrimitiveSamReaderToSamReaderAdapter.getFilePointerSpanningReads() |
SAMFileSpan |
SAMFileReader.getFilePointerSpanningReads()
Deprecated.
Gets a pointer spanning all reads in the BAM file.
|
SAMFileSpan |
SRAFileReader.getFilePointerSpanningReads() |
SAMFileSpan |
SAMFileSpan.removeContentsBefore(SAMFileSpan fileSpan)
Remove all pointers in this file span before the given file span starts.
|
SAMFileSpan |
BAMFileSpan.removeContentsBefore(SAMFileSpan fileSpan)
Creates a new file span by removing all chunks before the given file span starts.
|
protected static SAMFileSpan |
BAMFileSpan.toChunkList(long[] coordinateArray)
The list of chunks is often represented as an array of
longs where every even-numbered index is a start coordinate
and every odd-numbered index is a stop coordinate.
|
Modifier and Type | Method and Description |
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CloseableIterator<SAMRecord> |
CRAMFileReader.getIterator(SAMFileSpan fileSpan) |
CloseableIterator<SAMRecord> |
SamReader.PrimitiveSamReader.getIterator(SAMFileSpan fileSpan) |
CloseableIterator<SAMRecord> |
SRAFileReader.getIterator(SAMFileSpan chunks) |
SAMRecordIterator |
CRAMFileReader.iterator(SAMFileSpan fileSpan) |
SAMRecordIterator |
SamReader.Indexing.iterator(SAMFileSpan chunks)
Iterate through the given chunks in the file.
|
SAMRecordIterator |
SamReader.PrimitiveSamReaderToSamReaderAdapter.iterator(SAMFileSpan chunks) |
SAMRecordIterator |
SAMFileReader.iterator(SAMFileSpan chunks)
Deprecated.
Iterate through the given chunks in the file.
|
SAMRecordIterator |
SAMFileTruncatedReader.iterator(SAMFileSpan chunks)
Deprecated.
|
SAMRecordIterator |
SRAFileReader.iterator(SAMFileSpan chunks)
Iterate through the given chunks in the file.
|
SAMFileSpan |
SAMFileSpan.removeContentsBefore(SAMFileSpan fileSpan)
Remove all pointers in this file span before the given file span starts.
|
SAMFileSpan |
BAMFileSpan.removeContentsBefore(SAMFileSpan fileSpan)
Creates a new file span by removing all chunks before the given file span starts.
|
Constructor and Description |
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SAMFileSource(SamReader reader,
SAMFileSpan filePointer)
Create a new SAMFileSource with the given reader and file pointer.
|