ExtReadHit.java

package org.seqcode.deepseq;

import org.seqcode.genome.Genome;

public class ExtReadHit extends ReadHit {

	public ExtReadHit(Genome g, ReadHit r, int startShift, int fivePrimeExt, int threePrimeExt) {
		super(r.getChrom(), 
				r.getStrand() == '+' ? Math.max(1, r.getStart()+startShift-fivePrimeExt) : Math.max(1,r.getStart()-startShift-threePrimeExt) ,
				r.getStrand() == '+' ? Math.min(g.getChromLength(r.getChrom()), r.getEnd()+startShift+threePrimeExt) : Math.min(g.getChromLength(r.getChrom()), r.getEnd()-startShift+fivePrimeExt),
						r.getStrand(),r.getWeight());
	}

}