pro.parseq.vcf.utils

Class VcfParserImpl

java.lang.Object

pro.parseq.vcf.utils.VcfParserImpl

All Implemented Interfaces:

VcfParser

public class VcfParserImpl
extends Object
implements VcfParser

VcfParser implementation based on VCFv4.2 specification

Author:

Alexander Afanasyev aafanasyev@parseq.pro

Constructor Summary

Constructors

Constructor and Description
VcfParserImpl()

Method Summary

Modifier and Type	Method and Description
VcfFile	parse(VcfReader reader, FaultTolerance mode) Parses input VCF file

Methods inherited from class java.lang.Object

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

Constructor Detail

VcfParserImpl

public VcfParserImpl()

Method Detail

parse

public VcfFile parse(VcfReader reader,
                     FaultTolerance mode)
              throws InvalidVcfFileException

Description copied from interface: VcfParser

Parses input VCF file

Specified by:

parse in interface VcfParser

Parameters:

reader - VCF file reader

mode - Parsing mode (can be switched to fail fast or fail safe)

Returns:

VcfFile representing VCF file data

Throws:

InvalidVcfFileException - if input VCF file is malformed