org.seqdoop.hadoop_bam

Enum SAMFormat

java.lang.Object

java.lang.Enum<SAMFormat>

org.seqdoop.hadoop_bam.SAMFormat

All Implemented Interfaces:

Serializable, Comparable<SAMFormat>

public enum SAMFormat
extends Enum<SAMFormat>

Describes a SAM format.

Enum Constant Summary

Enum Constants

Enum Constant and Description
BAM
CRAM
SAM

Method Summary

Modifier and Type	Method and Description
static SAMFormat	inferFromData(InputStream in)
static SAMFormat	inferFromFilePath(org.apache.hadoop.fs.Path path) Infers the SAM format by looking at the filename of the given path.
static SAMFormat	inferFromFilePath(String name) Infers the SAM format by looking at the extension of the given file name.
static SAMFormat	valueOf(String name) Returns the enum constant of this type with the specified name.
static SAMFormat[]	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

SAM

public static final SAMFormat SAM

BAM

public static final SAMFormat BAM

CRAM

public static final SAMFormat CRAM

Method Detail

values

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

Returns:

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

valueOf

public static SAMFormat 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 name

NullPointerException - if the argument is null

inferFromFilePath

public static SAMFormat inferFromFilePath(org.apache.hadoop.fs.Path path)

Infers the SAM format by looking at the filename of the given path.

See Also:

inferFromFilePath(String)

inferFromFilePath

public static SAMFormat inferFromFilePath(String name)

Infers the SAM format by looking at the extension of the given file name. *.sam is recognized as SAM, *.bam as BAM, and *.bam as CRAM.

inferFromData

public static SAMFormat inferFromData(InputStream in)
                               throws IOException

Throws:

IOException