Package org.broadinstitute.hellbender.utils.haplotype

Enum Class HaplotypeBAMWriter.WriterType

java.lang.Object

java.lang.Enum<HaplotypeBAMWriter.WriterType>

org.broadinstitute.hellbender.utils.haplotype.HaplotypeBAMWriter.WriterType

All Implemented Interfaces:

Serializable, Comparable<HaplotypeBAMWriter.WriterType>, Constable

Enclosing class:

HaplotypeBAMWriter

public static enum HaplotypeBAMWriter.WriterType
extends Enum<HaplotypeBAMWriter.WriterType>

Possible modes for writing haplotypes to BAMs

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
ALL_POSSIBLE_HAPLOTYPES	A mode that's for method developers.
CALLED_HAPLOTYPES	A mode for users.
CALLED_HAPLOTYPES_NO_READS	Same as CALLED_HAPLOTYPES, but without reads
NO_HAPLOTYPES	With this option, haplotypes will not be included in the output bam.

Method Summary

Modifier and Type	Method	Description
static HaplotypeBAMWriter.WriterType	valueOf(String name)	Returns the enum constant of this class with the specified name.
static HaplotypeBAMWriter.WriterType[]	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

ALL_POSSIBLE_HAPLOTYPES

public static final HaplotypeBAMWriter.WriterType ALL_POSSIBLE_HAPLOTYPES

A mode that's for method developers. Writes out all of the possible haplotypes considered, as well as reads aligned to each

CALLED_HAPLOTYPES

public static final HaplotypeBAMWriter.WriterType CALLED_HAPLOTYPES

A mode for users. Writes out the reads aligned only to the called haplotypes. Useful to understand why the caller is calling what it is

NO_HAPLOTYPES

public static final HaplotypeBAMWriter.WriterType NO_HAPLOTYPES

With this option, haplotypes will not be included in the output bam.

CALLED_HAPLOTYPES_NO_READS

public static final HaplotypeBAMWriter.WriterType CALLED_HAPLOTYPES_NO_READS

Same as CALLED_HAPLOTYPES, but without reads

Method Details

values

public static HaplotypeBAMWriter.WriterType[] 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 HaplotypeBAMWriter.WriterType 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