/*
 * 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.genotyper;

import org.broad.tribble.util.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.*;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.commandline.Output;

import java.util.Collection;
import java.io.PrintWriter;

/**
 * Creates a bed-format trigger-track for the Unified Genotyper based on input variant files.
 */
public class CreateTriggerTrack extends RodWalker<Integer, Integer> {
    @Output
    private PrintWriter writer;

    public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
        if ( tracker == null )
            return 0;

        Collection<VariantContext> VCs = tracker.getAllVariantContexts(ref);
        if ( VCs.size() > 0 )
            writer.println(context.getLocation().getContig() + "\t" + context.getLocation().getStart() + "\t" + context.getLocation().getStart());

        return 0;
    }

    public Integer reduceInit() { return 0; }

    public Integer reduce(Integer value, Integer sum) { return 0; }

    public void onTraversalDone(Integer result) {
        writer.close();
    }
}
@@ -2137,32 +2137,33 @@
 ntig() + %22%5Ct%22 + 
+(
 context.getLocat
@@ -2178,16 +2178,19 @@
 tStart()
+-1)
  + %22%5Ct%22 

Properly output .bed