org.snpeff.vcf.VariantVcfEntry 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.vcf;

import java.util.Collection;
import java.util.LinkedList;

import org.snpeff.interval.Variant;

/**
 * Variant + VcfEntry
 * This is used to 'outer-join' a VcfEntry into all its constituent variants.
 *
 * IMPORTANT: The reason why we need this is because a VcfEntry may have
 * multiple variants (e.g. multiallelic entry). These entries may need
 * to be added multiple times to different nodes in an interval tree.
 *
 * @author pcingola
 */
public class VariantVcfEntry extends Variant {

	private static final long serialVersionUID = 2589022632388179932L;

	protected VcfEntry vcfEntry;

	/**
	 * Create a collection of all 
	 */
	public static Collection factory(VcfEntry vcfEntry) {
		LinkedList list = new LinkedList<>();

		for (Variant var : vcfEntry.variants())
			list.add(new VariantVcfEntry(var, vcfEntry));

		return list;
	}

	public VariantVcfEntry(Variant variant, VcfEntry vcfEntry) {
		super(variant.getParent(), variant.getStart(), variant.getEnd(), variant.getId());

		chromosomeNameOri = variant.getChromosomeNameOri();
		type = variant.getType();
		variantType = variant.getVariantType();
		ref = variant.getReference();
		alt = variant.getAlt();
		genotype = variant.getGenotype();
		imprecise = variant.isImprecise();

		this.vcfEntry = vcfEntry;
	}

	public VcfEntry getVcfEntry() {
		return vcfEntry;
	}

	@Override
	public String toString() {
		return "Variant: " + super.toString() + "\tVcfEntry: " + vcfEntry;
	}
}