org.snpeff.probablility.RandMarker 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.probablility;

import java.util.Random;

import org.snpeff.interval.Chromosome;
import org.snpeff.interval.Genome;
import org.snpeff.interval.Marker;

/**
 * Create random markers using a uniform distribution
 * 
 * @author pcingola
 */
public class RandMarker {

	Random rand;
	Genome genome;
	long genomeSize;

	public RandMarker(Genome genome) {
		rand = new Random();
		this.genome = genome;
		init();
	}

	public RandMarker(Genome genome, int seed) {
		rand = new Random(seed);
		this.genome = genome;
		init();
	}

	/**
	 * Initialize
	 */
	void init() {
		genomeSize = 0;
		for (Chromosome chr : genome)
			genomeSize += chr.size();
	}

	/**
	 * Create a random marker of size readLen
	 * @param readLen
	 * 
	 * WARNIIG: It will loop forever if there is no chromosome longer than readLen
	 * 
	 * @return A marker at a random chromosome & position.
	 */
	public Marker rand(int readLen) {
		while (true) {
			Marker m = random(readLen);
			if (m != null) return m;
		}
	}

	/**
	 * Create a random marker of size readLen
	 * @param readLen
	 * @return A marker at a random chromosome & position. Can be null sometimes
	 */
	Marker random(int readLen) {
		// Random number
		long chrPos = Math.abs(rand.nextLong()) % genomeSize;

		//---
		// Select a chromosome
		//---
		long pos = chrPos;
		Chromosome chromo = null;
		for (Chromosome chr : genome) {
			if (pos <= chr.size()) {
				chromo = chr;
				break;
			}
			pos -= chr.size();
		}
		if (chromo == null) throw new RuntimeException("Selected null chromosome. This should never happen!");
		if (pos < 0) throw new RuntimeException("Negative position. This should never happen!");
		if ((pos + readLen) > chromo.size()) return null; // Read pass chromosome length (can happen)

		return new Marker(chromo, (int) pos, (int) (pos + readLen - 1), false, "");
	}
}