org.seqdoop.hadoop_bam

Enum VCFFormat

java.lang.Object

java.lang.Enum<VCFFormat>

org.seqdoop.hadoop_bam.VCFFormat

All Implemented Interfaces:

Serializable, Comparable<VCFFormat>

public enum VCFFormat
extends Enum<VCFFormat>

Describes a VCF format.

Enum Constant Summary

Enum Constants

Enum Constant and Description
BCF
VCF

Method Summary

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

VCF

public static final VCFFormat VCF

BCF

public static final VCFFormat BCF

Method Detail

values

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

Returns:

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

valueOf

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

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

See Also:

inferFromFilePath(String)

inferFromFilePath

public static VCFFormat inferFromFilePath(String name)

Infers the VCF format by looking at the extension of the given file name. *.vcf is recognized as VCF and *.bcf as BCF.

inferFromData

public static VCFFormat inferFromData(InputStream in)
                               throws IOException

Infers the VCF format by looking at the first few bytes of the input.

Throws:

IOException

isGzip

public static boolean isGzip(InputStream in)
                      throws IOException

Returns:

true if the stream is compressed with gzip (or BGZF)

Throws:

IOException