org.pharmgkb.parser.vcf

Class MemoryMappedVcfLineParser

java.lang.Object

org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser

All Implemented Interfaces:

VcfLineParser

public class MemoryMappedVcfLineParser
extends java.lang.Object
implements VcfLineParser

A simple VcfLineParser that loads an entire VCF file into memory to permit constant-time lookup for VCF records, either:

• By any ID listed in the ID field, or
• By chromosome and position

This implementation is memory-intensive and should only be used for short VCF files where repeated arbitrary (random) access to VCF records is required.

By default, an IllegalArgumentException is thrown each time a duplicate ID or locus is found. To change this behavior, see MemoryMappedVcfLineParser.Builder.setDuplicateLocusHandler(org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.DuplicateHandler) and MemoryMappedVcfLineParser.Builder.setDuplicateLocusHandler(org.pharmgkb.parser.vcf.MemoryMappedVcfLineParser.DuplicateHandler).

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	MemoryMappedVcfLineParser.Builder
static class	MemoryMappedVcfLineParser.DuplicateHandler What to do when a duplicate VCF record (line) is encountered.

Method Summary

Modifier and Type	Method and Description
MemoryMappedVcfDataStore	getDataStore()
void	parseLine(VcfMetadata metadata, VcfPosition position, java.util.List<VcfSample> sampleData)

Methods inherited from class java.lang.Object

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

Method Detail

getDataStore

@Nonnull
public MemoryMappedVcfDataStore getDataStore()

parseLine

public void parseLine(VcfMetadata metadata,
                      VcfPosition position,
                      java.util.List<VcfSample> sampleData)

Specified by:

parseLine in interface VcfLineParser