Package htsjdk.samtools
Enum SamReaderFactory.Option
- java.lang.Object
-
- java.lang.Enum<SamReaderFactory.Option>
-
- htsjdk.samtools.SamReaderFactory.Option
-
- All Implemented Interfaces:
Serializable
,Comparable<SamReaderFactory.Option>
- Enclosing class:
- SamReaderFactory
public static enum SamReaderFactory.Option extends Enum<SamReaderFactory.Option>
A collection of binarySamReaderFactory
options.
-
-
Enum Constant Summary
Enum Constants Enum Constant Description 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.DONT_MEMORY_MAP_INDEX
The factory'sSamReader
s' will not use memory mapping for accessing index files (which is used by default).EAGERLY_DECODE
INCLUDE_SOURCE_IN_RECORDS
The factory'sSamReader
s will produce populated (non-null) values when callingSAMRecord.getFileSource()
.VALIDATE_CRC_CHECKSUMS
ForSamReader
s backed by block-compressed streams, enable CRC validation of those streams.
-
Field Summary
Fields Modifier and Type Field Description static EnumSet<SamReaderFactory.Option>
DEFAULTS
-
Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static SamReaderFactory.Option
valueOf(String name)
Returns the enum constant of this type with the specified name.static SamReaderFactory.Option[]
values()
Returns an array containing the constants of this enum type, in the order they are declared.
-
-
-
Enum Constant Detail
-
INCLUDE_SOURCE_IN_RECORDS
public static final SamReaderFactory.Option INCLUDE_SOURCE_IN_RECORDS
The factory'sSamReader
s will produce populated (non-null) values when callingSAMRecord.getFileSource()
. This option increases memory footprint slightly perSAMRecord
.
-
CACHE_FILE_BASED_INDEXES
public static final SamReaderFactory.Option 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.
-
DONT_MEMORY_MAP_INDEX
public static final SamReaderFactory.Option 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.
-
EAGERLY_DECODE
public static final SamReaderFactory.Option EAGERLY_DECODE
-
VALIDATE_CRC_CHECKSUMS
public static final SamReaderFactory.Option 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.
-
-
Field Detail
-
DEFAULTS
public static final EnumSet<SamReaderFactory.Option> DEFAULTS
-
-
Method Detail
-
values
public static SamReaderFactory.Option[] values()
Returns an array containing the constants of this enum type, in the order they are declared. This method may be used to iterate over the constants as follows:for (SamReaderFactory.Option c : SamReaderFactory.Option.values()) System.out.println(c);
- Returns:
- an array containing the constants of this enum type, in the order they are declared
-
valueOf
public static SamReaderFactory.Option valueOf(String name)
Returns the enum constant of this type with the specified name. The string must match exactly an identifier used to declare an enum constant in this type. (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 type has no constant with the specified nameNullPointerException
- if the argument is null
-
-