htsjdk.beta.plugin.reads

Class ReadsDecoderOptions

java.lang.Object

htsjdk.beta.plugin.reads.ReadsDecoderOptions

All Implemented Interfaces:

HtsDecoderOptions

public class ReadsDecoderOptions
extends java.lang.Object
implements HtsDecoderOptions

Reads decoder options (shared/common).

Constructor Summary

Constructors

Constructor and Description
ReadsDecoderOptions()

Method Summary

Modifier and Type	Method and Description
BAMDecoderOptions	getBAMDecoderOptions() Get the BAMDecoderOptions for these options.
CRAMDecoderOptions	getCRAMDecoderOptions() Get the CRAMDecoderOptions for these options.
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>>	getReadsChannelTransformer() Get the channel transformer for the reads resource.
ValidationStringency	getValidationStringency() Get the ValidationStringency used for these options.
boolean	isDecodeEagerly() Get eagerly decoding state used for these options.
boolean	isFileBasedIndexCached() Get the file based index cache setting used for these options.
boolean	isMemoryMapIndexes() Get whether mapping indexes is enabled.
ReadsDecoderOptions	setBAMDecoderOptions(BAMDecoderOptions bamDecoderOptions) Set the BAMDecoderOptions used for these options.
ReadsDecoderOptions	setCRAMDecoderOptions(CRAMDecoderOptions cramDecoderOptions) Set the CRAMDecoderOptions for these ReadsDecoderOptions.
ReadsDecoderOptions	setDecodeEagerly(boolean eagerlyDecode) Set the eagerly decoding state used for these options.
ReadsDecoderOptions	setFileBasedIndexCached(boolean fileBasedIndexCached) Set id file based index caching is enabled for these options.
ReadsDecoderOptions	setIndexChannelTransformer(java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> indexChannelTransformer) Set the channel transformer for the index resource.
ReadsDecoderOptions	setMemoryMapIndexes(boolean memoryMapIndexes) Set whether memory mapping indexes is enabled.
ReadsDecoderOptions	setReadsChannelTransformer(java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> readsChannelTransformer) Set the channel transformer for the reads resource.
ReadsDecoderOptions	setValidationStringency(ValidationStringency validationStringency) Set the ValidationStringency used for these options.

Methods inherited from class java.lang.Object

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

Constructor Detail

ReadsDecoderOptions

public ReadsDecoderOptions()

Method Detail

getValidationStringency

public ValidationStringency getValidationStringency()

Get the ValidationStringency used for these options. Defaults to ValidationStringency.STRICT.

Returns:

the ValidationStringency used for these options

setValidationStringency

public ReadsDecoderOptions setValidationStringency(ValidationStringency validationStringency)

Set the ValidationStringency used for these options. Defaults value is ValidationStringency.STRICT.

Parameters:

validationStringency - the ValidationStringency used for these options

Returns:

updated ReadsDecoderOptions

isDecodeEagerly

public boolean isDecodeEagerly()

Get eagerly decoding state used for these options.

Returns:

true if eager decoding is enabled, otherwise false

setDecodeEagerly

public ReadsDecoderOptions setDecodeEagerly(boolean eagerlyDecode)

Set the eagerly decoding state used for these options.

Parameters:

eagerlyDecode - true if eagerly decode is set, otherwise false

Returns:

updated ReadsDecoderOptions

isFileBasedIndexCached

public boolean isFileBasedIndexCached()

Get the file based index cache setting used for these options.

Returns:

true if caching is enabled for index files, otherwise false

setFileBasedIndexCached

public ReadsDecoderOptions setFileBasedIndexCached(boolean fileBasedIndexCached)

Set id file based index caching is enabled for these options.

Parameters:

fileBasedIndexCached - true to enable caching, otherwise false

Returns:

updated ReadsDecoderOptions

isMemoryMapIndexes

public boolean isMemoryMapIndexes()

Get whether mapping indexes is enabled. Defaults to true.

Returns:

true if indexes are memory mapped, otherwise false

setMemoryMapIndexes

public ReadsDecoderOptions setMemoryMapIndexes(boolean memoryMapIndexes)

Set whether memory mapping indexes is enabled. Defaults to true.

Parameters:

memoryMapIndexes - true if indexes are memory mapped, otherwise false

Returns:

updated ReadsDecoderOptions

getBAMDecoderOptions

public BAMDecoderOptions getBAMDecoderOptions()

Get the BAMDecoderOptions for these options.

Returns:

the BAMDecoderOptions for these options

setBAMDecoderOptions

public ReadsDecoderOptions setBAMDecoderOptions(BAMDecoderOptions bamDecoderOptions)

Set the BAMDecoderOptions used for these options.

Parameters:

bamDecoderOptions - the BAMDecoderOptions for these ReadsDecoderOptions

Returns:

updated ReadsDecoderOptions

getCRAMDecoderOptions

public CRAMDecoderOptions getCRAMDecoderOptions()

Get the CRAMDecoderOptions for these options.

Returns:

the CRAMDecoderOptions for these options

setCRAMDecoderOptions

public ReadsDecoderOptions setCRAMDecoderOptions(CRAMDecoderOptions cramDecoderOptions)

Set the CRAMDecoderOptions for these ReadsDecoderOptions.

Parameters:

cramDecoderOptions - the CRAMDecoderOptions for these ReadsDecoderOptions

Returns:

updated ReadsDecoderOptions

getReadsChannelTransformer

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

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

Returns:

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

setReadsChannelTransformer

@InternalAPI
public ReadsDecoderOptions setReadsChannelTransformer(java.util.function.Function<java.nio.channels.SeekableByteChannel,java.nio.channels.SeekableByteChannel> readsChannelTransformer)

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

Parameters:

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

Returns:

updated ReadsDecoderOptions

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 ReadsDecoderOptions 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 ReadsDecoderOptions