htsjdk.beta.codecs.reads.bam

Class BAMDecoderOptions

java.lang.Object

htsjdk.beta.codecs.reads.bam.BAMDecoderOptions

public class BAMDecoderOptions
extends java.lang.Object

Decoder options specific to BAM decoders.

Constructor Summary

Constructors

Constructor and Description
BAMDecoderOptions()

Method Summary

Modifier and Type	Method and Description
InflaterFactory	getInflaterFactory() Get the InflaterFactory used for these options.
boolean	isAsyncIO() Determine if async IO is enabled for these options.
boolean	isValidateCRCChecksums() Determine whether validation of CRC checksums is enabled for these options.
BAMDecoderOptions	setAsyncIO(boolean asyncIO) Set whether async IO is enable for these options.
BAMDecoderOptions	setInflaterFactory(InflaterFactory inflaterFactory) Set the InflaterFactory to use for these options.
BAMDecoderOptions	setValidateCRCChecksums(boolean validateCRCChecksums) Set whether validation of CRC checksums should be enabled for these options.

Methods inherited from class java.lang.Object

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

Constructor Detail

BAMDecoderOptions

public BAMDecoderOptions()

Method Detail

getInflaterFactory

public InflaterFactory getInflaterFactory()

Get the InflaterFactory used for these options. Defaults to BlockGunzipper.getDefaultInflaterFactory().

Returns:

the InflaterFactory used for these options

setInflaterFactory

public BAMDecoderOptions setInflaterFactory(InflaterFactory inflaterFactory)

Set the InflaterFactory to use for these options. Defaults value is BlockGunzipper.getDefaultInflaterFactory().

Parameters:

inflaterFactory - inflater factory to use

Returns:

updated BAMDecoderOptions

isAsyncIO

public boolean isAsyncIO()

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

Returns:

true if async IO is enabled for these options

setAsyncIO

public BAMDecoderOptions setAsyncIO(boolean asyncIO)

Set whether async IO is enable for these options. Defaults value is Defaults.USE_ASYNC_IO_READ_FOR_SAMTOOLS.

Parameters:

asyncIO - true if async IO should be used, otherwise false

Returns:

updated BAMDecoderOptions

isValidateCRCChecksums

public boolean isValidateCRCChecksums()

Determine whether validation of CRC checksums is enabled for these options. Defaults to false.

Returns:

true if CRC validation is enabled, otherwise false

setValidateCRCChecksums

public BAMDecoderOptions setValidateCRCChecksums(boolean validateCRCChecksums)

Set whether validation of CRC checksums should be enabled for these options. Defaults value is false.

Parameters:

validateCRCChecksums - true to enable CRC validation, otherwise false

Returns:

updated BAMDecoderOptions