Package htsjdk.beta.codecs.reads.cram

Class CRAMDecoderOptions

java.lang.Object

htsjdk.beta.codecs.reads.cram.CRAMDecoderOptions

public class CRAMDecoderOptions
extends Object

Decoder options specific to CRAM decoders.

Constructor Summary

Constructors

Constructor	Description
CRAMDecoderOptions()

Method Summary

Modifier and Type	Method	Description
Optional<IOPath>	getReferencePath()	Get the reference path for these options.
Optional<CRAMReferenceSource>	getReferenceSource()	Get the CRAMReferenceSource for these options.
CRAMDecoderOptions	setReferencePath(IOPath referencePath)	Set the reference path for these options.
CRAMDecoderOptions	setReferenceSource(CRAMReferenceSource referenceSource)	Set the CRAMReferenceSource for these options.

Methods inherited from class java.lang.Object

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

Constructor Details

CRAMDecoderOptions

public CRAMDecoderOptions()

Method Details

getReferenceSource

public Optional<CRAMReferenceSource> getReferenceSource()

Get the CRAMReferenceSource for these options.

Returns:

the CRAMReferenceSource for these options, or Optional.empty() if none

setReferenceSource

public CRAMDecoderOptions setReferenceSource(CRAMReferenceSource referenceSource)

Set the CRAMReferenceSource for these options. Mutually exclusive with setReferencePath(IOPath), which must be set to null in order to set a CRAMReferenceSource.

Parameters:

referenceSource - the CRAMReferenceSource for these options. May be null.

Returns:

updated CRAMDecoderOptions

Throws:

IllegalArgumentException - if a reference path is already set on these options

getReferencePath

public Optional<IOPath> getReferencePath()

Get the reference path for these options.

Returns:

the reference path for these options, or Optional.empty() if none.

setReferencePath

public CRAMDecoderOptions setReferencePath(IOPath referencePath)

Set the reference path for these options. Mutually exclusive with setReferenceSource(CRAMReferenceSource), which must be set to null in order to set a reference path.

Parameters:

referencePath - The path to use. may be null.

Returns:

updated CRAMDecoderOptions

Throws:

IllegalArgumentException - if a reference source is already set on these options