Package 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 Object

Constructor Summary

Constructors

Constructor	Description
Builder()

Method Summary

Modifier and Type	Method	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 Details

Builder

public Builder()

Method Details

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()