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.InfoFieldAnnotation;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.StandardAnnotation;
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
import org.broadinstitute.sting.utils.codecs.vcf.VCFHeaderLineType;
import org.broadinstitute.sting.utils.codecs.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.variantcontext.VariantContext;

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


/**
 * Total count across all samples of mapping quality zero reads
 */
public class MappingQualityZero extends InfoFieldAnnotation implements StandardAnnotation {

    public Map<String, Object> annotate(RefMetaDataTracker tracker, AnnotatorCompatibleWalker walker, ReferenceContext ref, Map<String, AlignmentContext> stratifiedContexts, VariantContext vc) {
        if ( stratifiedContexts.size() == 0 )
            return null;

        int mq0 = 0;
        for ( Map.Entry<String, AlignmentContext> sample : stratifiedContexts.entrySet() ) {
            final AlignmentContext context = sample.getValue();
            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<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(getKeyNames().get(0), 1, VCFHeaderLineType.Integer, "Total Mapping Quality Zero Reads")); }
}