/*
 * Copyright (c) 2010, The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
 * restriction, including without limitation the rights to use,
 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 * OTHER DEALINGS IN THE SOFTWARE.
 */
package org.broadinstitute.sting.gatk.walkers.phasing;

import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;

import java.util.ArrayList;
import java.util.List;

public class AllelePair {
    private Allele top;
    private Allele bottom;

    public AllelePair(Genotype gt) {
        if (gt.getPloidy() != 2)
            throw new ReviewedStingException("AllelePair must have ploidy of 2!");

        this.top = gt.getAllele(0);
        this.bottom = gt.getAllele(1);
    }

    public Allele getTopAllele() {
        return top;
    }

    public Allele getBottomAllele() {
        return bottom;
    }

    public void swapAlleles() {
        Allele tmp = top;
        top = bottom;
        bottom = tmp;
    }

    public List<Allele> getAllelesAsList() {
        List<Allele> allList = new ArrayList<Allele>(2);
        allList.add(0, top);
        allList.add(1, bottom);
        return allList;
    }

    public String toString() {
        StringBuilder sb = new StringBuilder();
        sb.append("Top:\t" + top.getBaseString() + "\n");
        sb.append("Bot:\t" + bottom.getBaseString() + "\n");
        return sb.toString();
    }
}
/*
 * Copyright (c) 2010, The Broad Institute
 *
 * Permission is hereby granted, free of charge, to any person
 * obtaining a copy of this software and associated documentation
 * files (the "Software"), to deal in the Software without
 * restriction, including without limitation the rights to use,
 * copy, modify, merge, publish, distribute, sublicense, and/or sell
 * copies of the Software, and to permit persons to whom the
 * Software is furnished to do so, subject to the following
 * conditions:
 *
 * The above copyright notice and this permission notice shall be
 * included in all copies or substantial portions of the Software.
 * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
 * EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
 * OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
 * NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
 * HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
 * WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
 * FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
 * OTHER DEALINGS IN THE SOFTWARE.
 */
package org.broadinstitute.sting.gatk.walkers.phasing;

import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
import org.broadinstitute.sting.utils.variantcontext.Allele;
import org.broadinstitute.sting.utils.variantcontext.Genotype;

import java.util.ArrayList;
import java.util.List;

public class AllelePair {
    private Allele top;
    private Allele bottom;

    public AllelePair(Genotype gt) {
        if (gt.getPloidy() != 2)
            throw new ReviewedStingException("AllelePair must have ploidy of 2! incoming gt was"+gt.toBriefString());

        this.top = gt.getAllele(0);
        this.bottom = gt.getAllele(1);
    }

    public Allele getTopAllele() {
        return top;
    }

    public Allele getBottomAllele() {
        return bottom;
    }

    public void swapAlleles() {
        Allele tmp = top;
        top = bottom;
        bottom = tmp;
    }

    public List<Allele> getAllelesAsList() {
        List<Allele> allList = new ArrayList<Allele>(2);
        allList.add(0, top);
        allList.add(1, bottom);
        return allList;
    }

    public String toString() {
        StringBuilder sb = new StringBuilder();
        sb.append("Top:\t" + top.getBaseString() + "\n");
        sb.append("Bot:\t" + bottom.getBaseString() + "\n");
        return sb.toString();
    }
}
Allow segments of genome to be excluded in generating a reference panel. Occasionally targets would contain no variation (typically, in the middle of the centromere), which beagle doesn't particularly like, and errors out rather than producing empty output files. The best way to deal with these is to just exclude the regions on a second-pass, and the remaining bits will be gathered with no additional work.