Uses of Class
htsjdk.samtools.cram.ref.ReferenceSource

Packages that use ReferenceSource

Package	Description
htsjdk.samtools
htsjdk.samtools.cram.build
htsjdk.samtools.cram.ref

Uses of ReferenceSource in htsjdk.samtools

Methods in htsjdk.samtools that return ReferenceSource

Modifier and Type	Method and Description
abstract ReferenceSource	SamReaderFactory.referenceSource()

Methods in htsjdk.samtools with parameters of type ReferenceSource

Modifier and Type	Method and Description
abstract SamReaderFactory	SamReaderFactory.referenceSource(ReferenceSource referenceSequence) Sets the specified reference sequence *

Constructors in htsjdk.samtools with parameters of type ReferenceSource

Constructor and Description
CRAMContainerStreamWriter(java.io.OutputStream outputStream, java.io.OutputStream indexStream, ReferenceSource source, SAMFileHeader samFileHeader, java.lang.String cramId) Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.
CRAMFileReader(java.io.File cramFile, java.io.File indexFile, ReferenceSource referenceSource) Create a CRAMFileReader from a file and optional index file using the supplied reference source.
CRAMFileReader(java.io.File cramFile, java.io.File indexFile, ReferenceSource referenceSource, ValidationStringency validationStringency) Create a CRAMFileReader from a CRAM file and optional index file using the supplied reference source and validation stringency.
CRAMFileReader(java.io.File cramFile, java.io.InputStream inputStream, ReferenceSource referenceSource) Create a CRAMFileReader from either a file or input stream using the supplied reference source.
CRAMFileReader(java.io.File cramFile, ReferenceSource referenceSource) Create a CRAMFileReader from a file using the supplied reference source.
CRAMFileReader(java.io.InputStream stream, java.io.File indexFile, ReferenceSource referenceSource, ValidationStringency validationStringency) Create a CRAMFileReader from an input stream and optional index file using the supplied reference source and validation stringency.
CRAMFileReader(java.io.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.
CRAMFileWriter(java.io.OutputStream outputStream, java.io.OutputStream indexOS, boolean presorted, ReferenceSource referenceSource, SAMFileHeader samFileHeader, java.lang.String fileName) Create a CRAMFileWriter and optional index on output streams.
CRAMFileWriter(java.io.OutputStream outputStream, java.io.OutputStream indexOS, ReferenceSource referenceSource, SAMFileHeader samFileHeader, java.lang.String fileName) Create a CRAMFileWriter and optional index on output streams.
CRAMFileWriter(java.io.OutputStream outputStream, ReferenceSource referenceSource, 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)

Uses of ReferenceSource in htsjdk.samtools.cram.build

Constructors in htsjdk.samtools.cram.build with parameters of type ReferenceSource

Constructor and Description
CramNormalizer(SAMFileHeader header, ReferenceSource referenceSource)

Uses of ReferenceSource in htsjdk.samtools.cram.ref

Methods in htsjdk.samtools.cram.ref that return ReferenceSource

Modifier and Type	Method and Description
static ReferenceSource	ReferenceSource.getDefaultCRAMReferenceSource() Attempts to construct a default ReferenceSource for use with CRAM files when one has not been explicitly provided.