org.pharmgkb.parser.vcf

Enum MemoryMappedVcfLineParser.DuplicateHandler

java.lang.Object

java.lang.Enum<MemoryMappedVcfLineParser.DuplicateHandler>

org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.DuplicateHandler

All Implemented Interfaces:

java.io.Serializable, java.lang.Comparable<MemoryMappedVcfLineParser.DuplicateHandler>

Enclosing class:

MemoryMappedVcfLineParser

public static enum MemoryMappedVcfLineParser.DuplicateHandler
extends java.lang.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.

Enum Constant Summary

Enum Constants

Enum Constant and 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 and Description
static MemoryMappedVcfLineParser.DuplicateHandler	valueOf(java.lang.String name) Returns the enum constant of this type with the specified name.
static MemoryMappedVcfLineParser.DuplicateHandler[]	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

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 Detail

values

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

Returns:

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

valueOf

public static MemoryMappedVcfLineParser.DuplicateHandler 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