org.snpeff.snpEffect.factory.SnpEffPredictorFactoryGtf22 Maven / Gradle / Ivy

Go to download

Show more of this group Show more artifacts with this name
Show all versions of SnpEff Show documentation

Variant annotation and effect prediction package.

The newest version!

package org.snpeff.snpEffect.factory;

import org.snpeff.interval.Gtf2Marker;
import org.snpeff.snpEffect.Config;

/**
 * This class creates a SnpEffectPredictor from a GTF 2.2 file
 *
 * References: http://mblab.wustl.edu/GTF22.html
 *
 * @author pcingola
 */
public class SnpEffPredictorFactoryGtf22 extends SnpEffPredictorFactoryGff {

	public SnpEffPredictorFactoryGtf22(Config config) {
		super(config);
		version = "GTF22";
		fileName = config.getBaseFileNameGenes() + ".gtf";
	}

	@Override
	protected boolean parse(String line) {
		Gtf2Marker gffMarker = new Gtf2Marker(genome, line);
		return addInterval(gffMarker);
	}
}