htsjdk.samtools

Enum SamReaderFactory.Option

java.lang.Object

java.lang.Enum<SamReaderFactory.Option>

htsjdk.samtools.SamReaderFactory.Option

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<SamReaderFactory.Option>

Enclosing class:

SamReaderFactory

public static enum SamReaderFactory.Option
extends java.lang.Enum<SamReaderFactory.Option>

A collection of binary SamReaderFactory options.

Enum Constant Summary

Enum Constants

Enum Constant and Description
CACHE_FILE_BASED_INDEXES The factory's SamReaders' SamReader.indexing()'s calls to SamReader.Indexing.getIndex() will produce BAMIndexes 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 SamReaders' will not use memory mapping for accessing index files (which is used by default).
EAGERLY_DECODE Eagerly decode SamReader's SAMRecords, which can reduce memory footprint if many fields are being read per record, or if fields are going to be updated.
INCLUDE_SOURCE_IN_RECORDS The factory's SamReaders will produce populated (non-null) values when calling SAMRecord.getFileSource().
VALIDATE_CRC_CHECKSUMS For SamReaders backed by block-compressed streams, enable CRC validation of those streams.

Field Summary

Fields

Modifier and Type	Field and Description
static java.util.EnumSet<SamReaderFactory.Option>	DEFAULTS

Method Summary

Methods

Modifier and Type	Method and Description
static SamReaderFactory.Option	valueOf(java.lang.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.

Methods inherited from class java.lang.Enum

clone, compareTo, equals, finalize, getDeclaringClass, hashCode, name, ordinal, toString, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

INCLUDE_SOURCE_IN_RECORDS

public static final SamReaderFactory.Option INCLUDE_SOURCE_IN_RECORDS

The factory's SamReaders will produce populated (non-null) values when calling SAMRecord.getFileSource().

This option increases memory footprint slightly per SAMRecord.

CACHE_FILE_BASED_INDEXES

public static final SamReaderFactory.Option CACHE_FILE_BASED_INDEXES

The factory's SamReaders' SamReader.indexing()'s calls to SamReader.Indexing.getIndex() will produce BAMIndexes that do some caching in memory instead of reading the index from the disk for each query operation.

See Also:

SamReader.indexing(), SamReader.Indexing.getIndex()

DONT_MEMORY_MAP_INDEX

public static final SamReaderFactory.Option DONT_MEMORY_MAP_INDEX

The factory's SamReaders' 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:

SamReader.indexing(), SamReader.Indexing.getIndex()

EAGERLY_DECODE

public static final SamReaderFactory.Option EAGERLY_DECODE

Eagerly decode SamReader's SAMRecords, which can reduce memory footprint if many fields are being read per record, or if fields are going to be updated.

VALIDATE_CRC_CHECKSUMS

public static final SamReaderFactory.Option VALIDATE_CRC_CHECKSUMS

For SamReaders 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 java.util.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(java.lang.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:

java.lang.IllegalArgumentException - if this enum type has no constant with the specified name

java.lang.NullPointerException - if the argument is null