de.charite.compbio.jannovar.reference.VariantDescription Maven / Gradle / Ivy

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package de.charite.compbio.jannovar.reference;

import de.charite.compbio.jannovar.annotation.Annotation;

/**
 * Minimal description of a variant as triple (position, ref, alt).
 *
 * The reference and alternative allele string are returned as trimmed, first stripping common suffixes then common
 * prefixes. Note that this is not the same as normalized variants (see the link below) but allows for easier querying
 * in programs.
 *
 * @author Manuel Holtgrewe
 * @see 
 *      http://genome.sph.umich.edu/wiki/Variant_Normalization
 */
public interface VariantDescription {

	/** @return String with the canonical chromosome name */
	public String getChrName();

	/** @return integer identifying the chromosome */
	public int getChr();

	/** @return zero-based position of the variant on the chromosome */
	public int getPos();

	/**
	 * @return String with the reference allele in the variant, without common suffix or prefix to reference allele.
	 */
	public String getRef();

	/**
	 * @return String with the alternative allele in the variant, without common suffix or prefix to reference allele.
	 */
	public String getAlt();

	int compareTo(Annotation other);

}