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

Constructor Summary

Constructors

Constructor and Description
CRAMFileWriter(CRAMEncodingStrategy encodingStrategy, java.io.OutputStream outputStream, java.io.OutputStream indexOS, boolean presorted, CRAMReferenceSource referenceSource, SAMFileHeader samFileHeader, java.lang.String fileName) Create a CRAMFileWriter and optional index on output streams.
CRAMFileWriter(java.io.OutputStream outputStream, CRAMReferenceSource referenceSource, SAMFileHeader samFileHeader, java.lang.String fileName) Create a CRAMFileWriter on an output stream.
CRAMFileWriter(java.io.OutputStream outputStream, java.io.OutputStream indexOS, boolean presorted, CRAMReferenceSource 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, CRAMReferenceSource referenceSource, SAMFileHeader samFileHeader, java.lang.String fileName) Create a CRAMFileWriter and optional index on output streams.

Method Summary

Modifier and Type	Method and Description
protected void	finish() Do any required flushing here.
protected java.lang.String	getFilename() For producing error messages.
protected void	writeAlignment(SAMRecord alignment) Write an alignment record.
protected void	writeHeader(SAMFileHeader header) Write the header 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, getMaxRecordsInRam, getSortOrder, getTempDirectory, setDefaultMaxRecordsInRam, setHeader, setMaxRecordsInRam, setProgressLogger, setSortOrder, setSortOrderChecking, setTempDirectory

Methods inherited from class java.lang.Object

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

Constructor Detail

CRAMFileWriter

public CRAMFileWriter(java.io.OutputStream outputStream,
                      CRAMReferenceSource referenceSource,
                      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. Can not be null.

referenceSource - reference source. Can not be null.

samFileHeader - SAMFileHeader to be used. Can not be null. Sort order is determined by the sortOrder property of this arg.

fileName - used for display in error messages

Throws:

java.lang.IllegalArgumentException - if the outputStream, referenceSource or samFileHeader are null

CRAMFileWriter

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

Create a CRAMFileWriter and optional 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. Can not be null.

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

referenceSource - reference source

samFileHeader - SAMFileHeader to be used. Can not be null. Sort order is determined by the sortOrder property of this arg.

fileName - used for display in error messages

Throws:

java.lang.IllegalArgumentException - if the outputStream, referenceSource or samFileHeader are null

CRAMFileWriter

public CRAMFileWriter(java.io.OutputStream outputStream,
                      java.io.OutputStream indexOS,
                      boolean presorted,
                      CRAMReferenceSource referenceSource,
                      SAMFileHeader samFileHeader,
                      java.lang.String fileName)

Create a CRAMFileWriter and optional index on output streams.

Parameters:

outputStream - where to write the output. Can not be null.

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

referenceSource - reference source

samFileHeader - SAMFileHeader to be used. Can not be null. Sort order is determined by the sortOrder property of this arg.

fileName - used for display in error message display

Throws:

java.lang.IllegalArgumentException - if the outputStream, referenceSource or samFileHeader are null

CRAMFileWriter

public CRAMFileWriter(CRAMEncodingStrategy encodingStrategy,
                      java.io.OutputStream outputStream,
                      java.io.OutputStream indexOS,
                      boolean presorted,
                      CRAMReferenceSource referenceSource,
                      SAMFileHeader samFileHeader,
                      java.lang.String fileName)

Create a CRAMFileWriter and optional index on output streams.

Parameters:

encodingStrategy - encoding strategy to use when writing

outputStream - where to write the output. Can not be null.

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

referenceSource - reference source

samFileHeader - SAMFileHeader to be used. Can not be null. Sort order is determined by the sortOrder property of this arg.

fileName - used for display in error message display

Throws:

java.lang.IllegalArgumentException - if the outputStream, referenceSource or samFileHeader are null

Method Detail

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.

writeHeader

protected void writeHeader(SAMFileHeader header)

Description copied from class: SAMFileWriterImpl

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

IMPORTANT: this method will be abstract once SAMFileWriterImpl.writeHeader(String) is removed.

Note: default implementation uses SAMTextHeaderCodec.encode(java.io.Writer, htsjdk.samtools.SAMFileHeader) and calls SAMFileWriterImpl.writeHeader(String).

Overrides:

writeHeader in class SAMFileWriterImpl

Parameters:

header - object to write.

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.