pro.parseq.vcf

Class VcfExplorer

java.lang.Object

pro.parseq.vcf.VcfExplorer

public class VcfExplorer
extends Object

Main user-class for VCF parsing

Author:

Alexander Afanasyev aafanasyev@parseq.pro

Constructor Summary

Constructors

Constructor and Description
VcfExplorer(VcfReader reader, VcfParser parser)

Method Summary

Modifier and Type	Method and Description
VcfFile	getVcfData()
void	parse(FaultTolerance mode) Retrieve VCF file content from VCF reader.
void	setParser(VcfParser parser)
void	setReader(VcfReader reader)

Methods inherited from class java.lang.Object

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

Constructor Detail

VcfExplorer

public VcfExplorer(VcfReader reader,
                   VcfParser parser)

Method Detail

setReader

public void setReader(VcfReader reader)

setParser

public void setParser(VcfParser parser)

parse

public void parse(FaultTolerance mode)
           throws InvalidVcfFileException

Retrieve VCF file content from VCF reader. Should not throw exception with repeated calls.

Parameters:

mode - FaultTolerance

Throws:

InvalidVcfFileException

getVcfData

public VcfFile getVcfData()