Package org.pharmgkb.parser.vcf

Enum Class MemoryMappedVcfLineParser.DuplicateHandler

java.lang.Object

java.lang.Enum<MemoryMappedVcfLineParser.DuplicateHandler>

org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.DuplicateHandler

All Implemented Interfaces:

Serializable, Comparable<MemoryMappedVcfLineParser.DuplicateHandler>, Constable

Enclosing class:

MemoryMappedVcfLineParser

public static enum MemoryMappedVcfLineParser.DuplicateHandler
extends Enum<MemoryMappedVcfLineParser.DuplicateHandler>

What to do when a duplicate VCF record (line) is encountered. This includes cases where the contents of the record, such as the ALT, REF, INFO, and sample fields, differ.

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
FAIL	Return an IllegalArgumentException when a duplicate is encountered.
KEEP_FIRST	Always keep the record that was previously read.
KEEP_LAST	Replace the VcfSamples and VcfPosition.

Method Summary

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

FAIL

public static final MemoryMappedVcfLineParser.DuplicateHandler FAIL

Return an IllegalArgumentException when a duplicate is encountered.

KEEP_FIRST

public static final MemoryMappedVcfLineParser.DuplicateHandler KEEP_FIRST

Always keep the record that was previously read. That is, don't process duplicate records.

KEEP_LAST

public static final MemoryMappedVcfLineParser.DuplicateHandler KEEP_LAST

Replace the VcfSamples and VcfPosition. In other words, ignore the fact that the record is a duplicate and record it anyway.

Method Details

values

public static MemoryMappedVcfLineParser.DuplicateHandler[] 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 MemoryMappedVcfLineParser.DuplicateHandler 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