/*
 * 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.broad.tribble.vcf.VCFHeaderLineType;
import org.broad.tribble.vcf.VCFInfoHeaderLine;
import org.broadinstitute.sting.utils.collections.Pair;
import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
import org.broadinstitute.sting.utils.BaseUtils;
import org.broadinstitute.sting.utils.pileup.PileupElement;
import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;

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


public class SecondBaseSkew implements InfoFieldAnnotation, ExperimentalAnnotation {
    private final static double epsilon = Math.pow(10.0,-12.0);
    private final static String KEY_NAME = "2b_Chi";
    private final static double[] UNIFORM_ON_OFF_RATIO = {1.0/3.0, 2.0/3.0};
    private double[] proportionExpectations = UNIFORM_ON_OFF_RATIO;

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

    public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(KEY_NAME, 1, VCFHeaderLineType.Float, "Chi-square Secondary Base Skew")); }

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

        String annotation = getAnnotation(ref, stratifiedContexts, vc);
        if ( annotation == null )
            return null;
        Map<String, Object> map = new HashMap<String, Object>();
        map.put(getKeyNames().get(0), annotation);            
        return map;
    }

    public String getAnnotation(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
        if ( !vc.isBiallelic() || !vc.isSNP() )
            return null;

        char alternate = vc.getAlternateAllele(0).toString().charAt(0);

        Pair<Integer, Integer> depth = new Pair<Integer, Integer>(0, 0);
        for ( String sample : stratifiedContexts.keySet() ) {
            //Pair<Integer,Integer> sampleDepth = getSecondaryPileupNonrefCount(ref.getBase(),stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getPileup(), alternate);
            Pair<Integer, Integer> sampleDepth = getSecondaryPileupNonrefCount(ref.getBaseAsChar(), stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(), alternate);
            depth.first += sampleDepth.first;
            depth.second += sampleDepth.second;
        }

        if ( depth.first == 0 )
            return null;

        double biasedProportion = (1.0 + depth.second) / (1.0 + depth.first);
        double p_transformed = transform(biasedProportion, depth.first+1);
        double expected_transformed = transform(proportionExpectations[0], depth.first+1);
        double chi_square =  Math.signum(biasedProportion - proportionExpectations[0])*Math.min(Math.pow(p_transformed - expected_transformed, 2), Double.MAX_VALUE);
        return String.format("%f", chi_square);
    }

    private double transform( double proportion, int depth ) {
        proportion = proportion - epsilon;
        return proportion / ( Math.sqrt ( proportion*(1-proportion)/depth ) );
    }

    private Pair<Integer, Integer> getSecondaryPileupNonrefCount(char ref, ReadBackedPileup p, char snp ) {
        int variantDepth = 0;
        int variantsWithRefSecondBase = 0;

        for (PileupElement pile : p ) {
            byte pbase = pile.getBase();
            byte sbase = pile.getSecondBase();

            if ( BaseUtils.isRegularBase((char)sbase) && BaseUtils.basesAreEqual(pbase, (byte) snp) ) {
                variantDepth++;
                if ( BaseUtils.basesAreEqual(sbase, (byte)ref) ) {
                    variantsWithRefSecondBase++;
                }
            }
        }

        return new Pair<Integer, Integer>(variantDepth, variantsWithRefSecondBase);
    }
}