htsjdk.samtools

Class CRAMContainerStreamWriter

java.lang.Object

htsjdk.samtools.CRAMContainerStreamWriter

public class CRAMContainerStreamWriter
extends java.lang.Object

Class for writing SAMRecords into a series of CRAM containers on an output stream, with an optional index.

Constructor Summary

Constructors

Constructor and Description
CRAMContainerStreamWriter(CRAMEncodingStrategy encodingStrategy, CRAMReferenceSource referenceSource, SAMFileHeader samFileHeader, java.io.OutputStream outputStream, CRAMIndexer indexer, java.lang.String outputIdentifier) Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.
CRAMContainerStreamWriter(java.io.OutputStream outputStream, CRAMReferenceSource source, SAMFileHeader samFileHeader, java.lang.String outputIdentifier, CRAMIndexer indexer) Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.
CRAMContainerStreamWriter(java.io.OutputStream recordOutputStream, java.io.OutputStream indexOutputStream, CRAMReferenceSource source, SAMFileHeader samFileHeader, java.lang.String outputIdentifier) Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.

Method Summary

Modifier and Type	Method and Description
void	finish(boolean writeEOFContainer) Finish writing to the stream.
void	writeAlignment(SAMRecord alignment) Accumulate alignment records until we meet the threshold to flush a container.
protected void	writeContainer(Container container)
void	writeHeader() Write a CRAM file header and the previously provided SAM header to the stream.
void	writeHeader(SAMFileHeader requestedSAMFileHeader) Write a CRAM file header and the previously provided SAM header to the stream.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

CRAMContainerStreamWriter

public CRAMContainerStreamWriter(java.io.OutputStream recordOutputStream,
                                 java.io.OutputStream indexOutputStream,
                                 CRAMReferenceSource source,
                                 SAMFileHeader samFileHeader,
                                 java.lang.String outputIdentifier)

Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.

Parameters:

recordOutputStream - where to write the CRAM stream.

indexOutputStream - where to write the output index. Can be null if no index is required.

source - reference cramReferenceSource

samFileHeader - SAMFileHeader to be used. Sort order is determined by the sortOrder property of this arg.

outputIdentifier - used for display in error message display

CRAMContainerStreamWriter

public CRAMContainerStreamWriter(java.io.OutputStream outputStream,
                                 CRAMReferenceSource source,
                                 SAMFileHeader samFileHeader,
                                 java.lang.String outputIdentifier,
                                 CRAMIndexer indexer)

Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.

Parameters:

outputStream - where to write the CRAM stream.

source - reference cramReferenceSource

samFileHeader - SAMFileHeader to be used. Sort order is determined by the sortOrder property of this arg.

outputIdentifier - used for display in error message display

indexer - CRAM indexer. Can be null if no index is required.

CRAMContainerStreamWriter

public CRAMContainerStreamWriter(CRAMEncodingStrategy encodingStrategy,
                                 CRAMReferenceSource referenceSource,
                                 SAMFileHeader samFileHeader,
                                 java.io.OutputStream outputStream,
                                 CRAMIndexer indexer,
                                 java.lang.String outputIdentifier)

Create a CRAMContainerStreamWriter for writing SAM records into a series of CRAM containers on output stream, with an optional index.

Parameters:

encodingStrategy - encoding strategy values

referenceSource - reference cramReferenceSource

samFileHeader - SAMFileHeader to be used. Sort order is determined by the sortOrder property of this arg.

outputStream - where to write the CRAM stream.

indexer - CRAM indexer. Can be null if no index is required.

outputIdentifier - informational string included in error reporting

Method Detail

writeAlignment

public void writeAlignment(SAMRecord alignment)

Accumulate alignment records until we meet the threshold to flush a container.

Parameters:

alignment - must not be null

writeHeader

public void writeHeader(SAMFileHeader requestedSAMFileHeader)

Write a CRAM file header and the previously provided SAM header to the stream.

writeHeader

public void writeHeader()

Write a CRAM file header and the previously provided SAM header to the stream.

finish

public void finish(boolean writeEOFContainer)

Finish writing to the stream. Flushes the record cache and optionally emits an EOF container.

Parameters:

writeEOFContainer - true if an EOF container should be written. Only use false if writing a CRAM file fragment which will later be aggregated into a complete CRAM file.

writeContainer

protected void writeContainer(Container container)