/*
 * 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.annotator;

import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.AnnotatorCompatibleWalker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.GenotypeAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFFormatHeaderLine;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.Genotype;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;

import java.util.Arrays;
import java.util.HashMap;
import java.util.List;
import java.util.Map;

/**
 * Count for each sample of mapping quality zero reads
 */
public class MappingQualityZeroBySample extends GenotypeAnnotation {
    public Map<String, Object> annotate(RefMetaDataTracker tracker,
                                        AnnotatorCompatibleWalker walker, ReferenceContext ref, AlignmentContext context, VariantContext vc, Genotype g) {
        if ( g == null || !g.isCalled() )
            return null;

        int mq0 = 0;
        if ( context.hasBasePileup() ) {
            final ReadBackedPileup pileup = context.getBasePileup();
            for (PileupElement p : pileup ) {
                if ( p.getMappingQual() == 0 )
                    mq0++;
            }
        }
        Map<String, Object> map = new HashMap<String, Object>();
        map.put(getKeyNames().get(0), String.format("%d", mq0));
        return map;
    }

    public List<String> getKeyNames() { return Arrays.asList(VCFConstants.MAPPING_QUALITY_ZERO_KEY); }

    public List<VCFFormatHeaderLine> getDescriptions() { return Arrays.asList(
            new VCFFormatHeaderLine(getKeyNames().get(0), 1,
                    VCFHeaderLineType.Integer, "Number of Mapping Quality Zero Reads per sample")); }


}
