htsjdk.samtools

Class SAMFileWriterFactory

java.lang.Object

htsjdk.samtools.SAMFileWriterFactory

All Implemented Interfaces:

java.lang.Cloneable

public class SAMFileWriterFactory
extends java.lang.Object
implements java.lang.Cloneable

Create a writer for writing SAM, BAM, or CRAM files.

Constructor Summary

Constructors

Constructor and Description
SAMFileWriterFactory() simple constructor
SAMFileWriterFactory(SAMFileWriterFactory other) copy constructor

Method Summary

Modifier and Type	Method and Description
SAMFileWriterFactory	clone()
int	getCompressionLevel()
SAMFileWriter	makeBAMWriter(SAMFileHeader header, boolean presorted, java.io.File outputFile) Create a BAMFileWriter that is ready to receive SAMRecords.
SAMFileWriter	makeBAMWriter(SAMFileHeader header, boolean presorted, java.io.File outputFile, int compressionLevel) Create a BAMFileWriter that is ready to receive SAMRecords.
SAMFileWriter	makeBAMWriter(SAMFileHeader header, boolean presorted, java.io.OutputStream stream) Create a BAMFileWriter for writing to a stream that is ready to receive SAMRecords.
CRAMFileWriter	makeCRAMWriter(SAMFileHeader header, boolean presorted, java.io.File outputFile, java.io.File referenceFasta) Create a CRAMFileWriter on an output file.
CRAMFileWriter	makeCRAMWriter(SAMFileHeader header, java.io.File outputFile, java.io.File referenceFasta) Create a CRAMFileWriter on an output file.
CRAMFileWriter	makeCRAMWriter(SAMFileHeader header, java.io.OutputStream stream, java.io.File referenceFasta) Create a CRAMFileWriter on an output stream.
SAMFileWriter	makeSAMOrBAMWriter(SAMFileHeader header, boolean presorted, java.io.File outputFile) Create either a SAM or a BAM writer based on examination of the outputFile extension.
SAMFileWriter	makeSAMWriter(SAMFileHeader header, boolean presorted, java.io.File outputFile) Create a SAMTextWriter that is ready to receive SAMRecords.
SAMFileWriter	makeSAMWriter(SAMFileHeader header, boolean presorted, java.io.OutputStream stream) Create a SAMTextWriter for writing to a stream that is ready to receive SAMRecords.
SAMFileWriter	makeWriter(SAMFileHeader header, boolean presorted, java.io.File outputFile, java.io.File referenceFasta) Create a SAM, BAM or CRAM writer based on examination of the outputFile extension.
SAMFileWriterFactory	setAsyncOutputBufferSize(int asyncOutputBufferSize) If and only if using asynchronous IO then sets the maximum number of records that can be buffered per SAMFileWriter before producers will block when trying to write another SAMRecord.
SAMFileWriterFactory	setBufferSize(int bufferSize) Controls size of write buffer.
SAMFileWriterFactory	setCompressionLevel(int compressionLevel) set compression level 0!none 9: max
SAMFileWriterFactory	setCreateIndex(boolean setting) Convenience method allowing newSAMFileWriterFactory().setCreateIndex(true); Equivalent to SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(true); newSAMFileWriterFactory(); If a BAM or CRAM (not SAM) file is created, the setting is true, and the file header specifies coordinate order, then a BAM index file will be written along with the BAM file.
SAMFileWriterFactory	setCreateMd5File(boolean createMd5File) Sets whether to create md5Files for BAMs from this factory.
static void	setDefaultCreateIndexWhileWriting(boolean setting) Sets the default for subsequent SAMFileWriterFactories that do not specify whether to create an index.
static void	setDefaultCreateMd5File(boolean createMd5File) Sets the default for whether to create md5Files for BAM files this factory.
SAMFileWriterFactory	setDeflaterFactory(DeflaterFactory deflaterFactory) Set the deflater factory used by BAM writers created by this writer factory.
SAMFileWriterFactory	setMaxRecordsInRam(int maxRecordsInRam) Before creating a writer that is not presorted, this method may be called in order to override the default number of SAMRecords stored in RAM before spilling to disk (c.f.
SAMFileWriterFactory	setSamFlagFieldOutput(SamFlagField samFlagFieldOutput) Set the flag output format only when writing text.
SAMFileWriterFactory	setTempDirectory(java.io.File tmpDir) Set the temporary directory to use when sort data.
SAMFileWriterFactory	setUseAsyncIo(boolean useAsyncIo) Turn on or off the use of asynchronous IO for writing output SAM and BAM files.
java.lang.String	toString()

Methods inherited from class java.lang.Object

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

Constructor Detail

SAMFileWriterFactory

public SAMFileWriterFactory()

simple constructor

SAMFileWriterFactory

public SAMFileWriterFactory(SAMFileWriterFactory other)

copy constructor

Method Detail

clone

public SAMFileWriterFactory clone()

Overrides:

clone in class java.lang.Object

setDefaultCreateMd5File

public static void setDefaultCreateMd5File(boolean createMd5File)

Sets the default for whether to create md5Files for BAM files this factory.

setCreateMd5File

public SAMFileWriterFactory setCreateMd5File(boolean createMd5File)

Sets whether to create md5Files for BAMs from this factory.

setDeflaterFactory

public SAMFileWriterFactory setDeflaterFactory(DeflaterFactory deflaterFactory)

Set the deflater factory used by BAM writers created by this writer factory. Must not be null. If this method is not called, the default DeflaterFactory is used which creates the default JDK Deflater. This method returns the SAMFileWriterFactory itself.

setCompressionLevel

public SAMFileWriterFactory setCompressionLevel(int compressionLevel)

set compression level 0!none 9: max

getCompressionLevel

public int getCompressionLevel()

setDefaultCreateIndexWhileWriting

public static void setDefaultCreateIndexWhileWriting(boolean setting)

Sets the default for subsequent SAMFileWriterFactories that do not specify whether to create an index. If a BAM (not SAM) file is created, the setting is true, and the file header specifies coordinate order, then a BAM index file will be written along with the BAM file.

Parameters:

setting - whether to attempt to create a BAM index while creating the BAM file

setCreateIndex

public SAMFileWriterFactory setCreateIndex(boolean setting)

Convenience method allowing newSAMFileWriterFactory().setCreateIndex(true); Equivalent to SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(true); newSAMFileWriterFactory(); If a BAM or CRAM (not SAM) file is created, the setting is true, and the file header specifies coordinate order, then a BAM index file will be written along with the BAM file.

Parameters:

setting - whether to attempt to create a BAM index while creating the BAM file.

Returns:

this factory object

setMaxRecordsInRam

public SAMFileWriterFactory setMaxRecordsInRam(int maxRecordsInRam)

Before creating a writer that is not presorted, this method may be called in order to override the default number of SAMRecords stored in RAM before spilling to disk (c.f. SAMFileWriterImpl.MAX_RECORDS_IN_RAM). When writing very large sorted SAM files, you may need call this method in order to avoid running out of file handles. The RAM available to the JVM may need to be increased in order to hold the specified number of records in RAM. This value affects the number of records stored in subsequent calls to one of the make...() methods.

Parameters:

maxRecordsInRam - Number of records to store in RAM before spilling to temporary file when creating a sorted SAM or BAM file.

setUseAsyncIo

public SAMFileWriterFactory setUseAsyncIo(boolean useAsyncIo)

Turn on or off the use of asynchronous IO for writing output SAM and BAM files. If true then each SAMFileWriter creates a dedicated thread which is used for compression and IO activities.

setAsyncOutputBufferSize

public SAMFileWriterFactory setAsyncOutputBufferSize(int asyncOutputBufferSize)

If and only if using asynchronous IO then sets the maximum number of records that can be buffered per SAMFileWriter before producers will block when trying to write another SAMRecord.

setBufferSize

public SAMFileWriterFactory setBufferSize(int bufferSize)

Controls size of write buffer. Default value: [[htsjdk.samtools.Defaults#BUFFER_SIZE]]

setTempDirectory

public SAMFileWriterFactory setTempDirectory(java.io.File tmpDir)

Set the temporary directory to use when sort data.

Parameters:

tmpDir - Path to the temporary directory

setSamFlagFieldOutput

public SAMFileWriterFactory setSamFlagFieldOutput(SamFlagField samFlagFieldOutput)

Set the flag output format only when writing text. Default value: [[htsjdk.samtools.SAMTextWriter.samFlagFieldOutput.DECIMAL]]

makeBAMWriter

public SAMFileWriter makeBAMWriter(SAMFileHeader header,
                                   boolean presorted,
                                   java.io.File outputFile)

Create a BAMFileWriter that is ready to receive SAMRecords. Uses default compression level.

Parameters:

header - entire header. Sort order is determined by the sortOrder property of this arg.

presorted - if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.

outputFile - where to write the output.

makeBAMWriter

public SAMFileWriter makeBAMWriter(SAMFileHeader header,
                                   boolean presorted,
                                   java.io.File outputFile,
                                   int compressionLevel)

Create a BAMFileWriter that is ready to receive SAMRecords.

Parameters:

header - entire header. Sort order is determined by the sortOrder property of this arg.

presorted - if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.

outputFile - where to write the output.

compressionLevel - Override default compression level with the given value, between 0 (fastest) and 9 (smallest).

makeSAMWriter

public SAMFileWriter makeSAMWriter(SAMFileHeader header,
                                   boolean presorted,
                                   java.io.File outputFile)

Create a SAMTextWriter that is ready to receive SAMRecords.

Parameters:

header - entire header. Sort order is determined by the sortOrder property of this arg.

presorted - if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.

outputFile - where to write the output.

makeSAMWriter

public SAMFileWriter makeSAMWriter(SAMFileHeader header,
                                   boolean presorted,
                                   java.io.OutputStream stream)

Create a SAMTextWriter for writing to a stream that is ready to receive SAMRecords. This method does not support the creation of an MD5 file

Parameters:

header - entire header. Sort order is determined by the sortOrder property of this arg.

presorted - if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.

stream - the stream to write records to. Note that this method does not buffer the stream, so the caller must buffer if desired. Note that PrintStream is buffered.

makeBAMWriter

public SAMFileWriter makeBAMWriter(SAMFileHeader header,
                                   boolean presorted,
                                   java.io.OutputStream stream)

Create a BAMFileWriter for writing to a stream that is ready to receive SAMRecords. This method does not support the creation of an MD5 file

Parameters:

header - entire header. Sort order is determined by the sortOrder property of this arg.

presorted - if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.

stream - the stream to write records to. Note that this method does not buffer the stream, so the caller must buffer if desired. Note that PrintStream is buffered.

makeSAMOrBAMWriter

public SAMFileWriter makeSAMOrBAMWriter(SAMFileHeader header,
                                        boolean presorted,
                                        java.io.File outputFile)

Create either a SAM or a BAM writer based on examination of the outputFile extension.

Parameters:

header - entire header. Sort order is determined by the sortOrder property of this arg.

presorted - presorted if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.

outputFile - where to write the output. Must end with .sam or .bam.

Returns:

SAM or BAM writer based on file extension of outputFile.

makeWriter

public SAMFileWriter makeWriter(SAMFileHeader header,
                                boolean presorted,
                                java.io.File outputFile,
                                java.io.File referenceFasta)

Create a SAM, BAM or CRAM writer based on examination of the outputFile extension.

Parameters:

header - header. Sort order is determined by the sortOrder property of this arg.

presorted - if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.

outputFile - where to write the output. Must end with .sam, .bam or .cram.

referenceFasta - reference sequence file

Returns:

SAMFileWriter appropriate for the file type specified in outputFile

makeCRAMWriter

public CRAMFileWriter makeCRAMWriter(SAMFileHeader header,
                                     java.io.OutputStream stream,
                                     java.io.File referenceFasta)

Create a CRAMFileWriter on an output stream. Requires the input to be presorted to match the sort order defined by the input header. Note: does not honor factory settings for CREATE_MD5, CREATE_INDEX, USE_ASYNC_IO.

Parameters:

header - entire header. Sort order is determined by the sortOrder property of this arg.

stream - where to write the output.

referenceFasta - reference sequence file

Returns:

CRAMFileWriter

makeCRAMWriter

public CRAMFileWriter makeCRAMWriter(SAMFileHeader header,
                                     java.io.File outputFile,
                                     java.io.File referenceFasta)

Create a CRAMFileWriter on an output file. Requires input record to be presorted to match the sort order defined by the input header. Note: does not honor factory settings for USE_ASYNC_IO.

Parameters:

header - entire header. Sort order is determined by the sortOrder property of this arg.

outputFile - where to write the output. Must end with .sam, .bam or .cram.

referenceFasta - reference sequence file

Returns:

CRAMFileWriter

makeCRAMWriter

public CRAMFileWriter makeCRAMWriter(SAMFileHeader header,
                                     boolean presorted,
                                     java.io.File outputFile,
                                     java.io.File referenceFasta)

Create a CRAMFileWriter on an output file. Note: does not honor factory setting for USE_ASYNC_IO.

Parameters:

header - entire header. Sort order is determined by the sortOrder property of this arg.

presorted - if true, SAMRecords must be added to the SAMFileWriter in order that agrees with header.sortOrder.

outputFile - where to write the output. Must end with .sam, .bam or .cram.

referenceFasta - reference sequence file

Returns:

CRAMFileWriter

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object