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Library for Variant Call Format (VCF) files manipulation

There is a newer version: 1.1.1-RELEASE

/*******************************************************************************
 *     Copyright 2016-2017 the original author or authors.
 *
 *  Licensed under the Apache License, Version 2.0 (the "License");
 *  you may not use this file except in compliance with the License.
 *  You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 *  Unless required by applicable law or agreed to in writing, software
 *  distributed under the License is distributed on an "AS IS" BASIS,
 *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 *  See the License for the specific language governing permissions and
 *  limitations under the License.
 *  
 *******************************************************************************/
package pro.parseq.vcf;

import pro.parseq.vcf.exceptions.InvalidVcfFileException;
import pro.parseq.vcf.types.VcfFile;
import pro.parseq.vcf.utils.FaultTolerance;
import pro.parseq.vcf.utils.VcfParser;
import pro.parseq.vcf.utils.VcfReader;

/**
 * Main user-class for VCF parsing
 * 
 * @author Alexander Afanasyev [email protected]
 */
public class VcfExplorer {

	private VcfReader reader;
	private VcfParser parser;

	private VcfFile vcfData;

	public VcfExplorer(VcfReader reader, VcfParser parser) {
		this.reader = reader;
		this.parser = parser;
	}

	public void setReader(VcfReader reader) {
		this.reader = reader;
	}

	public void setParser(VcfParser parser) {
		this.parser = parser;
	}

	public void parse(FaultTolerance mode) throws InvalidVcfFileException {
		vcfData = parser.parse(reader, mode);
	}

	public VcfFile getVcfData() {
		return vcfData;
	}
}