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Variant annotation and effect prediction package.

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package org.snpeff.vcf;

import java.util.HashMap;
import java.util.Map;

import org.snpeff.fileIterator.VcfFileIterator;

/**
 * An 'CSQ' entry in a vcf header line
 *
 * @author pablocingolani
 */
public class VcfConsequenceHeader {

	VcfHeaderInfo vcfInfoCsq;
	String fieldNames[];
	Map fieldNum;

	public VcfConsequenceHeader(VcfFileIterator vcf) {
		parseCsqHeader(vcf);
	}

	public String[] getFieldNames() {
		return fieldNames;
	}

	public Integer getFieldNum(String fieldName) {
		return fieldNum.get(fieldName);
	}

	void parseCsqHeader(VcfFileIterator vcf) {
		vcfInfoCsq = vcf.getVcfHeader().getVcfHeaderInfo(VcfConsequence.VCF_INFO_CSQ_NAME);
		if (vcfInfoCsq == null) throw new RuntimeException("Cannot find " + VcfConsequence.VCF_INFO_CSQ_NAME + " in VCF header");

		String descr = vcfInfoCsq.getDescription();
		String fields = descr.substring(descr.lastIndexOf(':') + 1);
		fieldNames = fields.split("\\|");

		fieldNum = new HashMap();
		for (int i = 0; i < fieldNames.length; i++) {
			fieldNames[i] = fieldNames[i].trim();
			fieldNum.put(fieldNames[i], i);
		}
	}

	@Override
	public String toString() {
		StringBuilder sb = new StringBuilder();
		for (String name : fieldNames)
			sb.append("Field '" + name + "', number " + getFieldNum(name) + "\n");
		return sb.toString();
	}
}