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.

Field Summary

Fields

Modifier and Type	Field and Description
protected int	containerSize
protected int	recordsPerSlice

Constructor Summary

Constructors

Constructor and Description
CRAMContainerStreamWriter(java.io.OutputStream outputStream, java.io.OutputStream indexStream, CRAMReferenceSource 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.

Method Summary

Modifier and Type	Method and Description
void	finish(boolean writeEOFContainer) Finish writing to the stream.
protected void	flushContainer() Complete the current container and flush it to the output stream.
java.util.Set<java.lang.String>	getCaptureTags()
java.util.Set<java.lang.String>	getIgnoreTags()
java.util.List<PreservationPolicy>	getPreservationPolicies()
boolean	isCaptureAllTags()
boolean	isPreserveReadNames()
void	setCaptureAllTags(boolean captureAllTags)
void	setCaptureTags(java.util.Set<java.lang.String> captureTags)
void	setIgnoreTags(java.util.Set<java.lang.String> ignoreTags)
void	setPreserveReadNames(boolean preserveReadNames)
protected boolean	shouldFlushContainer(SAMRecord nextRecord) Decide if the current container should be completed and flushed.
void	writeAlignment(SAMRecord alignment) Write an alignment record.
void	writeHeader(SAMFileHeader header) Write a CRAM file header and SAM header to the stream.

Methods inherited from class java.lang.Object

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

Field Detail

recordsPerSlice

protected final int recordsPerSlice

containerSize

protected final int containerSize

Constructor Detail

CRAMContainerStreamWriter

public CRAMContainerStreamWriter(java.io.OutputStream outputStream,
                                 java.io.OutputStream indexStream,
                                 CRAMReferenceSource 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.

Parameters:

outputStream - where to write the CRAM stream.

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

source - reference source

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

cramId - used for display in error message display

Method Detail

writeAlignment

public void writeAlignment(SAMRecord alignment)

Write an alignment record.

Parameters:

alignment - must not be null

writeHeader

public void writeHeader(SAMFileHeader header)

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

Parameters:

header - SAMFileHeader to write

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.

isPreserveReadNames

public boolean isPreserveReadNames()

setPreserveReadNames

public void setPreserveReadNames(boolean preserveReadNames)

getPreservationPolicies

public java.util.List<PreservationPolicy> getPreservationPolicies()

isCaptureAllTags

public boolean isCaptureAllTags()

setCaptureAllTags

public void setCaptureAllTags(boolean captureAllTags)

getCaptureTags

public java.util.Set<java.lang.String> getCaptureTags()

setCaptureTags

public void setCaptureTags(java.util.Set<java.lang.String> captureTags)

getIgnoreTags

public java.util.Set<java.lang.String> getIgnoreTags()

setIgnoreTags

public void setIgnoreTags(java.util.Set<java.lang.String> ignoreTags)

shouldFlushContainer

protected boolean shouldFlushContainer(SAMRecord nextRecord)

Decide if the current container should be completed and flushed. The decision is based on a) number of records and b) if the reference sequence id has changed.

Parameters:

nextRecord - the record to be added into the current or next container

Returns:

true if the current container should be flushed and the following records should go into a new container; false otherwise.

flushContainer

protected void flushContainer()
                       throws java.lang.IllegalArgumentException,
                              java.lang.IllegalAccessException,
                              java.io.IOException

Complete the current container and flush it to the output stream.

Throws:

java.lang.IllegalArgumentException

java.lang.IllegalAccessException

java.io.IOException