Serializable
, Comparable<SamReaderFactory.Option>
public static enum SamReaderFactory.Option extends Enum<SamReaderFactory.Option>
SamReaderFactory
options.Enum Constant | Description |
---|---|
CACHE_FILE_BASED_INDEXES |
The factory's
SamReader s' SamReader.indexing() 's calls to SamReader.Indexing.getIndex() will produce
BAMIndex 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's
SamReader s' will not use memory mapping for accessing index files (which is used by default). |
EAGERLY_DECODE |
|
INCLUDE_SOURCE_IN_RECORDS |
The factory's
SamReader s will produce populated (non-null) values when calling SAMRecord.getFileSource() . |
VALIDATE_CRC_CHECKSUMS |
For
SamReader s backed by block-compressed streams, enable CRC validation of those streams. |
Modifier and Type | Field | Description |
---|---|---|
static EnumSet<SamReaderFactory.Option> |
DEFAULTS |
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.
|
public static final SamReaderFactory.Option INCLUDE_SOURCE_IN_RECORDS
SamReader
s will produce populated (non-null) values when calling SAMRecord.getFileSource()
.
This option increases memory footprint slightly per SAMRecord
.public static final SamReaderFactory.Option CACHE_FILE_BASED_INDEXES
SamReader
s' SamReader.indexing()
's calls to SamReader.Indexing.getIndex()
will produce
BAMIndex
es that do some caching in memory instead of reading the index from the disk for each query operation.public static final SamReaderFactory.Option DONT_MEMORY_MAP_INDEX
SamReader
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.public static final SamReaderFactory.Option EAGERLY_DECODE
public static final SamReaderFactory.Option VALIDATE_CRC_CHECKSUMS
SamReader
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.public static EnumSet<SamReaderFactory.Option> DEFAULTS
public static SamReaderFactory.Option[] values()
for (SamReaderFactory.Option c : SamReaderFactory.Option.values()) System.out.println(c);
public static SamReaderFactory.Option valueOf(String name)
name
- the name of the enum constant to be returned.IllegalArgumentException
- if this enum type has no constant with the specified nameNullPointerException
- if the argument is null