Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.cram | |
htsjdk.samtools.cram.build | |
htsjdk.samtools.example | |
htsjdk.samtools.seekablestream | |
htsjdk.samtools.util | |
htsjdk.tribble.readers |
Modifier and Type | Method and Description |
---|---|
static SeekableStream |
SamIndexes.asBaiSeekableStreamOrNull(SeekableStream inputStream,
SAMSequenceDictionary dictionary) |
Modifier and Type | Method and Description |
---|---|
static SeekableStream |
SamIndexes.asBaiSeekableStreamOrNull(SeekableStream inputStream,
SAMSequenceDictionary dictionary) |
static void |
CRAMIndexer.createIndex(SeekableStream stream,
File output,
Log log,
ValidationStringency validationStringency)
Generates a BAI index file from an input CRAM stream
|
SamInputResource |
SamInputResource.index(SeekableStream seekableStream)
Updates the index to point at the provided resource, then returns itself.
|
static SamInputResource |
SamInputResource.of(SeekableStream seekableStream)
Creates a
SamInputResource reading from the provided resource, with no index. |
static boolean |
SamStreams.sourceLikeBam(SeekableStream strm) |
Constructor and Description |
---|
AbstractBAMFileIndex(SeekableStream stream,
SAMSequenceDictionary dictionary) |
CRAMFileReader(InputStream inputStream,
SeekableStream indexInputStream,
ReferenceSource referenceSource,
ValidationStringency validationStringency)
Create a CRAMFileReader from an input stream and optional index stream using the supplied reference
source and validation stringency.
|
CRAMIterator(SeekableStream seekableStream,
ReferenceSource referenceSource,
long[] coordinates)
Deprecated.
|
CRAMIterator(SeekableStream seekableStream,
ReferenceSource referenceSource,
long[] coordinates,
ValidationStringency validationStringency) |
DiskBasedBAMFileIndex(SeekableStream stream,
SAMSequenceDictionary dictionary) |
SAMFileReader(SeekableStream strm,
File indexFile,
boolean eagerDecode)
Deprecated.
Read a BAM file via caller-supplied mechanism.
|
SAMFileReader(SeekableStream strm,
SeekableStream indexStream,
boolean eagerDecode)
Deprecated.
|
Modifier and Type | Method and Description |
---|---|
static SeekableStream |
CRAIIndex.openCraiFileAsBaiStream(File cramIndexFile,
SAMSequenceDictionary dictionary) |
static SeekableStream |
CRAIIndex.openCraiFileAsBaiStream(InputStream indexStream,
SAMSequenceDictionary dictionary) |
Modifier and Type | Method and Description |
---|---|
static CramSpanContainerIterator |
CramSpanContainerIterator.fromFileSpan(SeekableStream seekableStream,
long[] coordinates) |
Modifier and Type | Method and Description |
---|---|
static SeekableStream |
ExampleSamUsage.myIndexSeekableStream() |
Modifier and Type | Class and Description |
---|---|
class |
ByteArraySeekableStream
Created by vadim on 23/03/2015.
|
class |
SeekableBufferedStream
A wrapper class to provide buffered read access to a SeekableStream.
|
class |
SeekableFileStream |
class |
SeekableFTPStream
Unfortunately the seekable stream classes exist for both Tribble and Picard, and we need both.
|
class |
SeekableHTTPStream |
class |
SeekableMemoryStream |
Modifier and Type | Method and Description |
---|---|
SeekableStream |
ISeekableStreamFactory.getBufferedStream(SeekableStream stream)
Return a buffered
SeekableStream which wraps the input stream
using the default buffer size |
SeekableStream |
ISeekableStreamFactory.getBufferedStream(SeekableStream stream,
int bufferSize)
Return a buffered
SeekableStream which wraps the input stream |
SeekableStream |
ISeekableStreamFactory.getStreamFor(String path) |
SeekableStream |
ISeekableStreamFactory.getStreamFor(URL url) |
Modifier and Type | Method and Description |
---|---|
SeekableStream |
ISeekableStreamFactory.getBufferedStream(SeekableStream stream)
Return a buffered
SeekableStream which wraps the input stream
using the default buffer size |
SeekableStream |
ISeekableStreamFactory.getBufferedStream(SeekableStream stream,
int bufferSize)
Return a buffered
SeekableStream which wraps the input stream |
Constructor and Description |
---|
SeekableBufferedStream(SeekableStream stream) |
SeekableBufferedStream(SeekableStream stream,
int bufferSize) |
Modifier and Type | Method and Description |
---|---|
static SeekableStream |
IOUtil.maybeBufferedSeekableStream(File file) |
static SeekableStream |
IOUtil.maybeBufferedSeekableStream(SeekableStream stream) |
static SeekableStream |
IOUtil.maybeBufferedSeekableStream(SeekableStream stream,
int bufferSize) |
static SeekableStream |
IOUtil.maybeBufferedSeekableStream(URL url) |
Modifier and Type | Method and Description |
---|---|
static SeekableStream |
IOUtil.maybeBufferedSeekableStream(SeekableStream stream) |
static SeekableStream |
IOUtil.maybeBufferedSeekableStream(SeekableStream stream,
int bufferSize) |
Constructor and Description |
---|
BlockCompressedInputStream(SeekableStream strm)
For providing some arbitrary data source.
|
CoordSpanInputSteam(SeekableStream delegate,
long[] coords)
Wrap
SeekableStream to read only bytes within boundaries specified in the coords array. |
Constructor and Description |
---|
TabixReader(String fn,
SeekableStream stream) |
TabixReader(String fn,
String idxFn,
SeekableStream stream) |