Package htsjdk.beta.plugin.reads
Class ReadsDecoderOptions
java.lang.Object
htsjdk.beta.plugin.reads.ReadsDecoderOptions
- All Implemented Interfaces:
HtsDecoderOptions
Reads decoder options (shared/common).
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Constructor Summary
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Method Summary
Modifier and TypeMethodDescriptionGet theBAMDecoderOptions
for these options.Get theCRAMDecoderOptions
for these options.Get the channel transformer for the index resource.Get the channel transformer for the reads resource.Get theValidationStringency
used for these options.boolean
Get eagerly decoding state used for these options.boolean
Get the file based index cache setting used for these options.boolean
Get whether mapping indexes is enabled.setBAMDecoderOptions
(BAMDecoderOptions bamDecoderOptions) Set theBAMDecoderOptions
used for these options.setCRAMDecoderOptions
(CRAMDecoderOptions cramDecoderOptions) Set theCRAMDecoderOptions
for these ReadsDecoderOptions.setDecodeEagerly
(boolean eagerlyDecode) Set the eagerly decoding state used for these options.setFileBasedIndexCached
(boolean fileBasedIndexCached) Set id file based index caching is enabled for these options.setIndexChannelTransformer
(Function<SeekableByteChannel, SeekableByteChannel> indexChannelTransformer) Set the channel transformer for the index resource.setMemoryMapIndexes
(boolean memoryMapIndexes) Set whether memory mapping indexes is enabled.setReadsChannelTransformer
(Function<SeekableByteChannel, SeekableByteChannel> readsChannelTransformer) Set the channel transformer for the reads resource.setValidationStringency
(ValidationStringency validationStringency) Set theValidationStringency
used for these options.
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Constructor Details
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ReadsDecoderOptions
public ReadsDecoderOptions()
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Method Details
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getValidationStringency
Get theValidationStringency
used for these options. Defaults toValidationStringency.STRICT
.- Returns:
- the
ValidationStringency
used for these options
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setValidationStringency
Set theValidationStringency
used for these options. Defaults value isValidationStringency.STRICT
.- Parameters:
validationStringency
- theValidationStringency
used for these options- Returns:
- updated ReadsDecoderOptions
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isDecodeEagerly
public boolean isDecodeEagerly()Get eagerly decoding state used for these options.- Returns:
- true if eager decoding is enabled, otherwise false
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setDecodeEagerly
Set the eagerly decoding state used for these options.- Parameters:
eagerlyDecode
- true if eagerly decode is set, otherwise false- Returns:
- updated ReadsDecoderOptions
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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
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setFileBasedIndexCached
Set id file based index caching is enabled for these options.- Parameters:
fileBasedIndexCached
- true to enable caching, otherwise false- Returns:
- updated ReadsDecoderOptions
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isMemoryMapIndexes
public boolean isMemoryMapIndexes()Get whether mapping indexes is enabled. Defaults to true.- Returns:
- true if indexes are memory mapped, otherwise false
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setMemoryMapIndexes
Set whether memory mapping indexes is enabled. Defaults to true.- Parameters:
memoryMapIndexes
- true if indexes are memory mapped, otherwise false- Returns:
- updated ReadsDecoderOptions
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getBAMDecoderOptions
Get theBAMDecoderOptions
for these options.- Returns:
- the
BAMDecoderOptions
for these options
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setBAMDecoderOptions
Set theBAMDecoderOptions
used for these options.- Parameters:
bamDecoderOptions
- theBAMDecoderOptions
for these ReadsDecoderOptions- Returns:
- updated ReadsDecoderOptions
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getCRAMDecoderOptions
Get theCRAMDecoderOptions
for these options.- Returns:
- the
CRAMDecoderOptions
for these options
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setCRAMDecoderOptions
Set theCRAMDecoderOptions
for these ReadsDecoderOptions.- Parameters:
cramDecoderOptions
- theCRAMDecoderOptions
for these ReadsDecoderOptions- Returns:
- updated ReadsDecoderOptions
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getReadsChannelTransformer
@InternalAPI public Optional<Function<SeekableByteChannel,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()
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setReadsChannelTransformer
@InternalAPI public ReadsDecoderOptions setReadsChannelTransformer(Function<SeekableByteChannel, 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
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getIndexChannelTransformer
@InternalAPI public Optional<Function<SeekableByteChannel,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()
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setIndexChannelTransformer
@InternalAPI public ReadsDecoderOptions setIndexChannelTransformer(Function<SeekableByteChannel, 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
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