htsjdk.samtools

Class CRAMFileWriter

java.lang.Object

htsjdk.samtools.SAMFileWriterImpl

htsjdk.samtools.CRAMFileWriter

All Implemented Interfaces:

SAMFileWriter, java.io.Closeable, java.lang.AutoCloseable

public class CRAMFileWriter
extends SAMFileWriterImpl

Field Summary

Fields

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

Constructor Summary

Constructors

Constructor and Description
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.

Method Summary

Modifier and Type	Method and Description
protected void	finish() Do any required flushing here.
protected void	flushContainer() Complete the current container and flush it to the output stream.
java.util.Set<java.lang.String>	getCaptureTags()
protected java.lang.String	getFilename() For producing error messages.
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.
protected void	writeAlignment(SAMRecord alignment) Write an alignment record.
protected void	writeHeader(java.lang.String textHeader) Write the header to disk.

Methods inherited from class htsjdk.samtools.SAMFileWriterImpl

addAlignment, close, getDefaultMaxRecordsInRam, getFileHeader, getSortOrder, setDefaultMaxRecordsInRam, setHeader, setProgressLogger, setSortOrder

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

CRAMFileWriter

public CRAMFileWriter(java.io.OutputStream outputStream,
                      ReferenceSource source,
                      SAMFileHeader samFileHeader,
                      java.lang.String fileName)

Create a CRAMFileWriter on an output stream. Requires input records to be presorted to match the sort order defined by the input samFileHeader.

Parameters:

outputStream - where to write the output.

source - reference source

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

fileName - used for display in error messages

CRAMFileWriter

public 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. Requires input records to be presorted to match the sort order defined by the input samFileHeader.

Parameters:

outputStream - where to write the output.

indexOS - 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.

fileName - used for display in error messages

CRAMFileWriter

public 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.

Parameters:

outputStream - where to write the output.

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

presorted - if true records written to this writer must already be sorted in the order specified by the header

source - reference source

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

fileName - used for display in error message display

Method Detail

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

writeAlignment

protected void writeAlignment(SAMRecord alignment)

Write an alignment record.

Specified by:

writeAlignment in class SAMFileWriterImpl

Parameters:

alignment - must not be null and must have a valid SAMFileHeader.

writeHeader

protected void writeHeader(java.lang.String textHeader)

Description copied from class: SAMFileWriterImpl

Write the header to disk. Header object is available via getHeader().

Specified by:

writeHeader in class SAMFileWriterImpl

Parameters:

textHeader - for convenience if the implementation needs it.

finish

protected void finish()

Description copied from class: SAMFileWriterImpl

Do any required flushing here.

Specified by:

finish in class SAMFileWriterImpl

getFilename

protected java.lang.String getFilename()

Description copied from class: SAMFileWriterImpl

For producing error messages.

Specified by:

getFilename in class SAMFileWriterImpl

Returns:

Output filename, or null if there isn't one.

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)