htsjdk.beta.codecs.reads.bam

Class BAMEncoderOptions

java.lang.Object

htsjdk.beta.codecs.reads.bam.BAMEncoderOptions

public class BAMEncoderOptions
extends java.lang.Object

Encoder options specific to BAM encoders.

Field Summary

Fields

Modifier and Type	Field and Description
static int	DEAFULT_MAX_RECORDS_IN_RAM

Constructor Summary

Constructors

Constructor and Description
BAMEncoderOptions()

Method Summary

Modifier and Type	Method and Description
int	getAsyncOutputBufferSize() Get the async output buffer size used for these options.
int	getCompressionLevel() Set the compression level for these options.
DeflaterFactory	getDeflaterFactory() Get the DeflaterFactory for these options.
int	getMaxRecordsInRAM() Set the maximum records kept in RAM before spilling to disk for these options.
int	getOutputBufferSize() Get the output buffer size for these options.
IOPath	getTemporaryDirectory() Get the temporary directory path used for these options.
boolean	isAsyncIO() Determine if async IO is enabled for these options.
BAMEncoderOptions	setAsyncIO(boolean asyncIO) Set whether to enable async IO for these options.
BAMEncoderOptions	setAsyncOutputBufferSize(int asyncOutputBufferSize) Get the async output buffer size used for these options.
BAMEncoderOptions	setCompressionLevel(int compressionLevel) Set the compression level for these options.
BAMEncoderOptions	setDeflaterFactory(DeflaterFactory deflaterFactory) Set the DeflaterFactory for these options for these options.
BAMEncoderOptions	setMaxRecordsInRAM(int maxRecordsInRAM) Get the maximum records kept in RAM before spilling to disk for these options.
BAMEncoderOptions	setOutputBufferSize(int outputBufferSize) Set the buffer size for these options.
BAMEncoderOptions	setTemporaryDirectory(IOPath tempDirPath) Get the temporary directory path for these options.

Methods inherited from class java.lang.Object

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

Field Detail

DEAFULT_MAX_RECORDS_IN_RAM

public static final int DEAFULT_MAX_RECORDS_IN_RAM

See Also:

Constant Field Values

Constructor Detail

BAMEncoderOptions

public BAMEncoderOptions()

Method Detail

getOutputBufferSize

public int getOutputBufferSize()

Get the output buffer size for these options. This determines the size of the output stream buffer used when writing outputs. Default value is Defaults.BUFFER_SIZE.

Returns:

the buffer size for these options

setOutputBufferSize

public BAMEncoderOptions setOutputBufferSize(int outputBufferSize)

Set the buffer size for these options. This determines the size of the output stream buffer used when writing outputs. Defaults value is Defaults.BUFFER_SIZE.

Parameters:

outputBufferSize - the buffer size for these options

Returns:

updated options

isAsyncIO

public boolean isAsyncIO()

Determine if async IO is enabled for these options. Defaults to Defaults.USE_ASYNC_IO_WRITE_FOR_SAMTOOLS.

Returns:

true if async IO is enabled, otherwise false

setAsyncIO

public BAMEncoderOptions setAsyncIO(boolean asyncIO)

Set whether to enable async IO for these options.

Parameters:

asyncIO - true to enable async IO, false to disable.

Returns:

updated options

getAsyncOutputBufferSize

public int getAsyncOutputBufferSize()

Get the async output buffer size used for these options. If and only if using asynchronous IO sets the maximum number of records that can be buffered per writer before producers will block when trying to write another record. Defaults to AbstractAsyncWriter.DEFAULT_QUEUE_SIZE.

Returns:

async output buffer size used for these options

setAsyncOutputBufferSize

public BAMEncoderOptions setAsyncOutputBufferSize(int asyncOutputBufferSize)

Get the async output buffer size used for these options. If and only if using asynchronous IO, sets the maximum number of records that can be buffered per writer before producers will block when trying to write another record.

Parameters:

asyncOutputBufferSize - async output buffer size used for these options

Returns:

updated options

getTemporaryDirectory

public IOPath getTemporaryDirectory()

Get the temporary directory path used for these options. The temporary directory path is used for temporary files created during output sorting operations. Defaults value is IOUtil.getDefaultTmpDirPath().

Returns:

the temp directory path to use for these options

setTemporaryDirectory

public BAMEncoderOptions setTemporaryDirectory(IOPath tempDirPath)

Get the temporary directory path for these options. The temporary directory path is used for temporary files created during output sorting operations. Defaults value is IOUtil.getDefaultTmpDirPath().

Parameters:

tempDirPath - temporary directory path to use

Returns:

updated options

getCompressionLevel

public int getCompressionLevel()

Set the compression level for these options. Defaults value is BlockCompressedStreamConstants.DEFAULT_COMPRESSION_LEVEL. See BlockCompressedStreamConstants.DEFAULT_COMPRESSION_LEVEL

Returns:

the compression level for these options, 1 <= compressionLevel <= 9

setCompressionLevel

public BAMEncoderOptions setCompressionLevel(int compressionLevel)

Set the compression level for these options. Defaults value is BlockCompressedStreamConstants.DEFAULT_COMPRESSION_LEVEL.

Parameters:

compressionLevel - the compression level for these options, 1 <= compressionLevel <= 9

Returns:

updated options

getMaxRecordsInRAM

public int getMaxRecordsInRAM()

Set the maximum records kept in RAM before spilling to disk for these options. May be null. Default value is Maximum records in RAM determines the amount of memory used by the writer when sorting output during writing. When writing very large sorted SAM files, you may need use this option 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. Defaults value is DEAFULT_MAX_RECORDS_IN_RAM.

Returns:

the maximum records kept in ram before spilling to disk for these options

setMaxRecordsInRAM

public BAMEncoderOptions setMaxRecordsInRAM(int maxRecordsInRAM)

Get the maximum records kept in RAM before spilling to disk for these options. Maximum records in RAM determines the amount of memory used by the writer when sorting output during writing. When writing very large sorted SAM files, you may need use this option 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. Defaults value is DEAFULT_MAX_RECORDS_IN_RAM.

Parameters:

maxRecordsInRAM - the maximum records kept in ram before spilling to disk. may be null.

Returns:

updated options

getDeflaterFactory

public DeflaterFactory getDeflaterFactory()

Get the DeflaterFactory for these options. Default value is BlockCompressedOutputStream.getDefaultDeflaterFactory().

Returns:

the DeflaterFactory for these options

setDeflaterFactory

public BAMEncoderOptions setDeflaterFactory(DeflaterFactory deflaterFactory)

Set the DeflaterFactory for these options for these options. Default value is BlockCompressedOutputStream.getDefaultDeflaterFactory().

Parameters:

deflaterFactory - the DeflaterFactory for these options

Returns:

updated options