org.broadinstitute.hellbender.tools.spark.sv.evidence

Enum TemplateFragmentOrdinal

java.lang.Object

java.lang.Enum<TemplateFragmentOrdinal>

org.broadinstitute.hellbender.tools.spark.sv.evidence.TemplateFragmentOrdinal

All Implemented Interfaces:

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

public enum TemplateFragmentOrdinal
extends java.lang.Enum<TemplateFragmentOrdinal>

Indicates the ordinal of a fragment in a paired sequenced template.

Enum Constant Summary

Enum Constants

Enum Constant and Description
PAIRED_FIRST For the first and only first fragment in a paired sequenced template.
PAIRED_INTERIOR For inner fragments in a paired sequenced template.
PAIRED_SECOND For the second/last and only second/last fragment in a paired sequenced template.
PAIRED_UNKNOWN For fragment in paired sequenced templates with unknown ordinal.
UNPAIRED Ordinal for fragments in unpaired sequenced templates.

Method Summary

Modifier and Type	Method and Description
static TemplateFragmentOrdinal	forRead(GATKRead read)
java.lang.String	nameSuffix()
java.lang.String	toString()
static TemplateFragmentOrdinal	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static TemplateFragmentOrdinal[]	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, valueOf

Methods inherited from class java.lang.Object

getClass, notify, notifyAll, wait, wait, wait

Enum Constant Detail

UNPAIRED

public static final TemplateFragmentOrdinal UNPAIRED

Ordinal for fragments in unpaired sequenced templates.

PAIRED_UNKNOWN

public static final TemplateFragmentOrdinal PAIRED_UNKNOWN

For fragment in paired sequenced templates with unknown ordinal.

PAIRED_FIRST

public static final TemplateFragmentOrdinal PAIRED_FIRST

For the first and only first fragment in a paired sequenced template.

PAIRED_SECOND

public static final TemplateFragmentOrdinal PAIRED_SECOND

For the second/last and only second/last fragment in a paired sequenced template.

PAIRED_INTERIOR

public static final TemplateFragmentOrdinal PAIRED_INTERIOR

For inner fragments in a paired sequenced template.

Method Detail

values

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

Returns:

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

valueOf

public static TemplateFragmentOrdinal 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

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Enum<TemplateFragmentOrdinal>

nameSuffix

public java.lang.String nameSuffix()

forRead

public static TemplateFragmentOrdinal forRead(GATKRead read)