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

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) Writes the record to disk.
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)

CRAMFileWriter

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

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)

Description copied from class: SAMFileWriterImpl

Writes the record to disk. Sort order has been taken care of by the time this method is called.

Specified by:

writeAlignment in class SAMFileWriterImpl

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)