/*
* Copyright 2012-2015 Broad Institute, Inc.
* 
* 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,
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*/

package org.broadinstitute.gatk.engine.filters;

import htsjdk.samtools.SAMRecord;

/**
 * Filter out reads with mapping quality zero
 *
 * <p>This filter is intended to ensure that only reads that are likely
 * to be mapped in the right place, and therefore to be informative, will be used in analysis.</p>
 *
 * <h3>Usage example</h3>
 *
 * <pre>
 *     java -jar GenomeAnalysisTk.jar \
 *         -T ToolName \
 *         -R reference.fasta \
 *         -I input.bam \
 *         -o output.file \
 *         -rf MappingQualityZero
 * </pre>
 *
 * @author hanna
 * @version 0.1
 */

public class MappingQualityZeroFilter extends ReadFilter {
    public boolean filterOut(SAMRecord rec) {
        return (rec.getMappingQuality() == 0);
    }
}

