htsjdk.beta.plugin.variants

Class VariantsDecoderOptions

java.lang.Object

htsjdk.beta.plugin.variants.VariantsDecoderOptions

All Implemented Interfaces:

HtsDecoderOptions

public class VariantsDecoderOptions
extends java.lang.Object
implements HtsDecoderOptions

Constructor Summary

Constructors

Constructor and Description
VariantsDecoderOptions()

Method Summary

Modifier and Type	Method and Description
java.util.Optional<java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel>>	getIndexChannelTransformer() Get the channel transformer for the index resource.
java.util.Optional<java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel>>	getVariantsChannelTransformer() Get the channel transformer for the variants resource.
VariantsDecoderOptions	setIndexChannelTransformer(java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> indexChannelTransformer) Set the channel transformer for the index resource.
VariantsDecoderOptions	setVariantsChannelTransformer(java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> variantsChannelTransformer) Set the channel transformer for the variants resource.

Methods inherited from class java.lang.Object

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

Constructor Detail

VariantsDecoderOptions

public VariantsDecoderOptions()

Method Detail

getVariantsChannelTransformer

@InternalAPI
public java.util.Optional<java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel>> getVariantsChannelTransformer()

Get the channel transformer for the variants resource. The channel transformer can be used to implement prefetching for the variants input.

Returns:

the channel transformer for the reads resource if present, otherwise Optional.empty()

setVariantsChannelTransformer

@InternalAPI
public VariantsDecoderOptions setVariantsChannelTransformer(java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> variantsChannelTransformer)

Set the channel transformer for the variants resource. The channel transformer can be used to implement prefetching for the variants input.

Parameters:

variantsChannelTransformer - the channel transformer to be used. may be null

Returns:

updated VariantsDecoderOptions

getIndexChannelTransformer

@InternalAPI
public java.util.Optional<java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel>> getIndexChannelTransformer()

Get the channel transformer for the index resource. The channel transformer can be used to implement prefetching for the index input.

Returns:

the channel transformer for the index resource if present, otherwise Optional.empty()

setIndexChannelTransformer

@InternalAPI
public VariantsDecoderOptions setIndexChannelTransformer(java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> indexChannelTransformer)

Set the channel transformer for the index resource. The channel transformer can be used to implement prefetching for the index input.

Parameters:

indexChannelTransformer - the channel transformer to be used. may be null.

Returns:

updated VariantsDecoderOptions