htsjdk.samtools

Enum SamIndexes

java.lang.Object

java.lang.Enum<SamIndexes>

htsjdk.samtools.SamIndexes

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<SamIndexes>

public enum SamIndexes
extends java.lang.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.

Enum Constant Summary

Enum Constants

Enum Constant and Description
BAI
CRAI

Field Summary

Fields

Modifier and Type	Field and Description
java.lang.String	fileNameSuffix
byte[]	magic

Method Summary

Modifier and Type	Method and Description
static SeekableStream	asBaiSeekableStreamOrNull(SeekableStream inputStream, SAMSequenceDictionary dictionary)
static java.io.InputStream	asBaiStreamOrNull(java.io.InputStream inputStream, SAMSequenceDictionary dictionary)
static java.io.InputStream	openIndexFileAsBaiOrNull(java.io.File file, SAMSequenceDictionary dictionary)
static java.io.InputStream	openIndexUrlAsBaiOrNull(java.net.URL url, SAMSequenceDictionary dictionary)
static SamIndexes	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static SamIndexes[]	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

BAI

public static final SamIndexes BAI

CRAI

public static final SamIndexes CRAI

Field Detail

fileNameSuffix

public final java.lang.String fileNameSuffix

magic

public final byte[] magic

Method Detail

values

public static SamIndexes[] 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 (SamIndexes c : SamIndexes.values())
    System.out.println(c);

Returns:

an array containing the constants of this enum type, in the order they are declared

valueOf

public static SamIndexes 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

openIndexFileAsBaiOrNull

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

Throws:

java.io.IOException

openIndexUrlAsBaiOrNull

public static java.io.InputStream openIndexUrlAsBaiOrNull(java.net.URL url,
                                                          SAMSequenceDictionary dictionary)
                                                   throws java.io.IOException

Throws:

java.io.IOException

asBaiStreamOrNull

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

Throws:

java.io.IOException

asBaiSeekableStreamOrNull

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

Throws:

java.io.IOException