Package htsjdk.samtools

Enum Class SamIndexes

java.lang.Object

java.lang.Enum<SamIndexes>

htsjdk.samtools.SamIndexes

All Implemented Interfaces:

Serializable, Comparable<SamIndexes>, Constable

public enum SamIndexes
extends Enum<SamIndexes>

A helper class to read BAI and CRAI indexes. Main goal is to provide BAI stream as a sort of common API for all index types.

Created by vadim on 14/08/2015.

Nested Class Summary

Nested classes/interfaces inherited from class java.lang.Enum

Enum.EnumDesc<E extends Enum<E>>

Enum Constant Summary

Enum Constants

Enum Constant	Description
BAI
CRAI
CSI

Field Summary

Fields

Modifier and Type	Field	Description
final String	fileNameSuffix
final byte[]	magic

Method Summary

Modifier and Type	Method	Description
static SeekableStream	asBaiSeekableStreamOrNull(SeekableStream inputStream, SAMSequenceDictionary dictionary)
static InputStream	asBaiStreamOrNull(InputStream inputStream, SAMSequenceDictionary dictionary)
static SamIndexes	getSAMIndexTypeFromStream(SeekableStream seekableStream)
static InputStream	openIndexFileAsBaiOrNull(File file, SAMSequenceDictionary dictionary)
static InputStream	openIndexUrlAsBaiOrNull(URL url, SAMSequenceDictionary dictionary)
static SamIndexes	valueOf(String name)	Returns the enum constant of this class with the specified name.
static SamIndexes[]	values()	Returns an array containing the constants of this enum class, in the order they are declared.

Methods inherited from class java.lang.Enum

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

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Details

BAI

public static final SamIndexes BAI

CRAI

public static final SamIndexes CRAI

CSI

public static final SamIndexes CSI

Field Details

fileNameSuffix

public final String fileNameSuffix

magic

public final byte[] magic

Method Details

values

public static SamIndexes[] 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

valueOf

public static SamIndexes valueOf(String name)

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 name

NullPointerException - if the argument is null

openIndexFileAsBaiOrNull

public static InputStream openIndexFileAsBaiOrNull(File file,
 SAMSequenceDictionary dictionary)
                                            throws IOException

Throws:

IOException

openIndexUrlAsBaiOrNull

public static InputStream openIndexUrlAsBaiOrNull(URL url,
 SAMSequenceDictionary dictionary)
                                           throws IOException

Throws:

IOException

asBaiStreamOrNull

public static InputStream asBaiStreamOrNull(InputStream inputStream,
 SAMSequenceDictionary dictionary)
                                     throws IOException

Throws:

IOException

asBaiSeekableStreamOrNull

public static SeekableStream asBaiSeekableStreamOrNull(SeekableStream inputStream,
 SAMSequenceDictionary dictionary)
                                                throws IOException

Throws:

IOException

getSAMIndexTypeFromStream

public static SamIndexes getSAMIndexTypeFromStream(SeekableStream seekableStream)