htsjdk.beta.plugin.reads

Class ReadsEncoderOptions

java.lang.Object

htsjdk.beta.plugin.reads.ReadsEncoderOptions

All Implemented Interfaces:

HtsEncoderOptions

public class ReadsEncoderOptions
extends java.lang.Object
implements HtsEncoderOptions

General reads encoder options.

Constructor Summary

Constructors

Constructor and Description
ReadsEncoderOptions()

Method Summary

Modifier and Type	Method and Description
BAMEncoderOptions	getBAMEncoderOptions() Get the BAMEncoderOptions for these ReadsEncoderOptions.
CRAMEncoderOptions	getCRAMEncoderOptions() Get the CRAMEncoderOptions for this ReadsEncoderOptions.
boolean	isPreSorted() Get the preSorted setting for these options.
ReadsEncoderOptions	setBAMEncoderOptions(BAMEncoderOptions bamEncoderOptions) Set the BAMEncoderOptions for these ReadsEncoderOptions.
ReadsEncoderOptions	setCRAMEncoderOptions(CRAMEncoderOptions cramEncoderOptions) Set the CRAMEncoderOptions for these ReadsEncoderOptions.
ReadsEncoderOptions	setPreSorted(boolean preSorted) Set the preSorted setting for these options.

Methods inherited from class java.lang.Object

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

Constructor Detail

ReadsEncoderOptions

public ReadsEncoderOptions()

Method Detail

isPreSorted

public boolean isPreSorted()

Get the preSorted setting for these options. Default value is false. If isPresorted is false, output will be sorted as needed on write.

Returns:

true if preSorted is true, otherwise false

setPreSorted

public ReadsEncoderOptions setPreSorted(boolean preSorted)

Set the preSorted setting for these options. Default value is false. If preSorted is false, output will be sorted as needed on write.

Parameters:

preSorted - the preSorted state for these options

Returns:

updated ReadsEncoderOptions

getBAMEncoderOptions

public BAMEncoderOptions getBAMEncoderOptions()

Get the BAMEncoderOptions for these ReadsEncoderOptions. Defaults to default BAMEncoderOptions.

Returns:

the BAMEncoderOptions for these ReadsEncoderOptions

setBAMEncoderOptions

public ReadsEncoderOptions setBAMEncoderOptions(BAMEncoderOptions bamEncoderOptions)

Set the BAMEncoderOptions for these ReadsEncoderOptions. Defaults values are default BAMEncoderOptions.

Parameters:

bamEncoderOptions - BAMEncoderOptions to use for these ReadsEncoderOptions

Returns:

updated ReadsEncoderOptions

getCRAMEncoderOptions

public CRAMEncoderOptions getCRAMEncoderOptions()

Get the CRAMEncoderOptions for this ReadsEncoderOptions. Default values are default CRAMEncoderOptions.

Returns:

the CRAMEncoderOptions for this ReadsEncoderOptions

setCRAMEncoderOptions

public ReadsEncoderOptions setCRAMEncoderOptions(CRAMEncoderOptions cramEncoderOptions)

Set the CRAMEncoderOptions for these ReadsEncoderOptions. Defaults to default CRAMEncoderOptions.

Parameters:

cramEncoderOptions - the CRAMEncoderOptions for these ReadsEncoderOptions

Returns:

updated ReadsEncoderOptions