org.pharmgkb.parser.vcf

Class MemoryMappedVcfLineParser.Builder

java.lang.Object

org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.Builder

Enclosing class:

MemoryMappedVcfLineParser

public static class MemoryMappedVcfLineParser.Builder
extends java.lang.Object

Constructor Summary

Constructors

Constructor and Description
Builder()

Method Summary

Modifier and Type	Method and Description
MemoryMappedVcfLineParser	build()
MemoryMappedVcfLineParser.Builder	setDuplicateIdHandler(MemoryMappedVcfLineParser.DuplicateHandler handler) Determines what to do when an ID that was previously set is encountered, regardless of whether the two IDs correspond to the same locus.
MemoryMappedVcfLineParser.Builder	setDuplicateLocusHandler(MemoryMappedVcfLineParser.DuplicateHandler handler) Determines what to do when a VCF record is encountered with a locus (chromosome and position) that was already found.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

Builder

public Builder()

Method Detail

setDuplicateIdHandler

@Nonnull
public MemoryMappedVcfLineParser.Builder setDuplicateIdHandler(@Nonnull
                                                                         MemoryMappedVcfLineParser.DuplicateHandler handler)

Determines what to do when an ID that was previously set is encountered, regardless of whether the two IDs correspond to the same locus. This is independent of #setDuplicateLocusHandler(DuplicateHandler), except when either is set to MemoryMappedVcfLineParser.DuplicateHandler.FAIL.

setDuplicateLocusHandler

@Nonnull
public MemoryMappedVcfLineParser.Builder setDuplicateLocusHandler(@Nonnull
                                                                            MemoryMappedVcfLineParser.DuplicateHandler handler)

Determines what to do when a VCF record is encountered with a locus (chromosome and position) that was already found. This is independent of #setDuplicateIdHandler(DuplicateHandler), except when either is set to MemoryMappedVcfLineParser.DuplicateHandler.FAIL.

build

public MemoryMappedVcfLineParser build()