Package htsjdk.samtools
Enum Class SamReaderFactory.Option
- All Implemented Interfaces:
Serializable
,Comparable<SamReaderFactory.Option>
,Constable
- Enclosing class:
SamReaderFactory
A collection of binary
SamReaderFactory
options.-
Nested Class Summary
Nested classes/interfaces inherited from class java.lang.Enum
Enum.EnumDesc<E extends Enum<E>>
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Enum Constant Summary
Enum ConstantsEnum ConstantDescriptionThe factory'sSamReader
s'SamReader.indexing()
's calls toSamReader.Indexing.getIndex()
will produceBAMIndex
es that do some caching in memory instead of reading the index from the disk for each query operation.The factory'sSamReader
s' will not use memory mapping for accessing index files (which is used by default).The factory'sSamReader
s will produce populated (non-null) values when callingSAMRecord.getFileSource()
.ForSamReader
s backed by block-compressed streams, enable CRC validation of those streams. -
Field Summary
Fields -
Method Summary
Modifier and TypeMethodDescriptionstatic SamReaderFactory.Option
Returns the enum constant of this class with the specified name.static SamReaderFactory.Option[]
values()
Returns an array containing the constants of this enum class, in the order they are declared.
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Enum Constant Details
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INCLUDE_SOURCE_IN_RECORDS
The factory'sSamReader
s will produce populated (non-null) values when callingSAMRecord.getFileSource()
. This option increases memory footprint slightly perSAMRecord
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CACHE_FILE_BASED_INDEXES
The factory'sSamReader
s'SamReader.indexing()
's calls toSamReader.Indexing.getIndex()
will produceBAMIndex
es that do some caching in memory instead of reading the index from the disk for each query operation.- See Also:
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DONT_MEMORY_MAP_INDEX
The factory'sSamReader
s' will not use memory mapping for accessing index files (which is used by default). This is slower but more scalable when accessing large numbers of BAM files sequentially.- See Also:
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EAGERLY_DECODE
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VALIDATE_CRC_CHECKSUMS
ForSamReader
s backed by block-compressed streams, enable CRC validation of those streams. This is an expensive operation, but serves to ensure validity of the stream.
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Field Details
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DEFAULTS
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Method Details
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values
Returns an array containing the constants of this enum class, in the order they are declared.- Returns:
- an array containing the constants of this enum class, in the order they are declared
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valueOf
Returns the enum constant of this class with the specified name. The string must match exactly an identifier used to declare an enum constant in this class. (Extraneous whitespace characters are not permitted.)- Parameters:
name
- the name of the enum constant to be returned.- Returns:
- the enum constant with the specified name
- Throws:
IllegalArgumentException
- if this enum class has no constant with the specified nameNullPointerException
- if the argument is null
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