<commit_before>package org.broadinstitute.sting.gatk;

import net.sf.samtools.SAMRecord;

import java.util.List;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.TreeSet;
import java.util.Random;

import org.broadinstitute.sting.utils.GenomeLoc;
import edu.mit.broad.picard.reference.ReferenceSequence;

/**
 * Useful class for forwarding on locusContext data from this iterator
 * 
 * Created by IntelliJ IDEA.
 * User: mdepristo
 * Date: Feb 22, 2009
 * Time: 3:01:34 PM
 * To change this template use File | Settings | File Templates.
 */
public class LocusContext {
    private GenomeLoc loc = null;
    private List<SAMRecord> reads = null;
    private List<Integer> offsets = null;
    private ReferenceSequence refContig = null;

    /**
     * Create a new LocusContext object
     *
     * @param loc
     * @param reads
     * @param offsets
     */
    public LocusContext(GenomeLoc loc, List<SAMRecord> reads, List<Integer> offsets) {
        this.loc = loc;
        this.reads = reads;
        this.offsets = offsets;
    }

    /**
     * get all of the reads within this context
     * 
     * @return<commit_msg>Added lots of assertions to check for problems.<commit_after>package org.broadinstitute.sting.gatk;

import net.sf.samtools.SAMRecord;

import java.util.List;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.TreeSet;
import java.util.Random;

import org.broadinstitute.sting.utils.GenomeLoc;
import edu.mit.broad.picard.reference.ReferenceSequence;

/**
 * Useful class for forwarding on locusContext data from this iterator
 * 
 * Created by IntelliJ IDEA.
 * User: mdepristo
 * Date: Feb 22, 2009
 * Time: 3:01:34 PM
 * To change this template use File | Settings | File Templates.
 */
public class LocusContext {
    private GenomeLoc loc = null;
    private List<SAMRecord> reads = null;
    private List<Integer> offsets = null;
    private ReferenceSequence refContig = null;

    /**
     * Create a new LocusContext object
     *
     * @param loc
     * @param reads
     * @param offsets
     */
    public LocusContext(GenomeLoc loc, List<SAMRecord> reads, List<Integer> offsets) {
        assert loc != null;
        assert loc.getContig() != null;
        assert reads != null;
        assert offsets != null;

        this.loc = loc;
        this.reads = reads;
        this.offsets = offsets;
    }

    /**
     * get all of the reads within this context
     * 
     * @return
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