Package | Description |
---|---|
htsjdk.samtools | |
htsjdk.samtools.cram.build |
Modifier and Type | Method and Description |
---|---|
abstract ReferenceSource |
SamReaderFactory.referenceSource() |
Modifier and Type | Method and Description |
---|---|
abstract SamReaderFactory |
SamReaderFactory.referenceSource(ReferenceSource referenceSequence)
Sets the specified reference sequence *
|
Constructor and Description |
---|
CRAMFileReader(java.io.File cramFile,
java.io.File indexFile,
ReferenceSource referenceSource)
Open CRAM file for reading.
|
CRAMFileReader(java.io.File cramFile,
java.io.File indexFile,
ReferenceSource referenceSource,
ValidationStringency validationStringency) |
CRAMFileReader(java.io.File cramFile,
java.io.InputStream inputStream,
ReferenceSource referenceSource)
Open CRAM data for reading using either the file or the input stream
supplied in the arguments.
|
CRAMFileReader(java.io.File cramFile,
ReferenceSource referenceSource) |
CRAMFileReader(java.io.InputStream stream,
java.io.File indexFile,
ReferenceSource referenceSource,
ValidationStringency validationStringency) |
CRAMFileReader(java.io.InputStream inputStream,
SeekableStream indexInputStream,
ReferenceSource referenceSource,
ValidationStringency validationStringency) |
CRAMFileWriter(java.io.OutputStream outputStream,
java.io.OutputStream indexOS,
boolean presorted,
ReferenceSource source,
SAMFileHeader samFileHeader,
java.lang.String fileName)
Create a CRAMFileWriter and index on output streams.
|
CRAMFileWriter(java.io.OutputStream outputStream,
java.io.OutputStream indexOS,
ReferenceSource source,
SAMFileHeader samFileHeader,
java.lang.String fileName)
Create a CRAMFileWriter and index on output streams.
|
CRAMFileWriter(java.io.OutputStream outputStream,
ReferenceSource source,
SAMFileHeader samFileHeader,
java.lang.String fileName)
Create a CRAMFileWriter on an output stream.
|
CRAMIterator(java.io.InputStream inputStream,
ReferenceSource referenceSource,
ValidationStringency validationStringency) |
CRAMIterator(SeekableStream seekableStream,
ReferenceSource referenceSource,
long[] coordinates)
Deprecated.
|
CRAMIterator(SeekableStream seekableStream,
ReferenceSource referenceSource,
long[] coordinates,
ValidationStringency validationStringency) |
Constructor and Description |
---|
CramNormalizer(SAMFileHeader header,
ReferenceSource referenceSource) |