116 lines
5.3 KiB
Java
Executable File
116 lines
5.3 KiB
Java
Executable File
/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.annotator;
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import org.broad.tribble.vcf.VCFHeaderLineType;
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import org.broad.tribble.vcf.VCFInfoHeaderLine;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.pileup.ReadBackedPileup;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.pileup.PileupElement;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.StratifiedAlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.annotator.interfaces.*;
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import java.util.Map;
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import java.util.HashMap;
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import java.util.List;
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import java.util.Arrays;
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public class SecondBaseSkew implements InfoFieldAnnotation, ExperimentalAnnotation {
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private final static double epsilon = Math.pow(10.0,-12.0);
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private final static String KEY_NAME = "2b_Chi";
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private final static double[] UNIFORM_ON_OFF_RATIO = {1.0/3.0, 2.0/3.0};
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private double[] proportionExpectations = UNIFORM_ON_OFF_RATIO;
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public List<String> getKeyNames() { return Arrays.asList(KEY_NAME); }
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public List<VCFInfoHeaderLine> getDescriptions() { return Arrays.asList(new VCFInfoHeaderLine(KEY_NAME, 1, VCFHeaderLineType.Float, "Chi-square Secondary Base Skew")); }
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public Map<String, Object> annotate(RefMetaDataTracker tracker, ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
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if ( stratifiedContexts.size() == 0 )
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return null;
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String annotation = getAnnotation(ref, stratifiedContexts, vc);
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if ( annotation == null )
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return null;
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Map<String, Object> map = new HashMap<String, Object>();
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map.put(getKeyNames().get(0), annotation);
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return map;
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}
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public String getAnnotation(ReferenceContext ref, Map<String, StratifiedAlignmentContext> stratifiedContexts, VariantContext vc) {
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if ( !vc.isBiallelic() || !vc.isSNP() )
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return null;
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char alternate = vc.getAlternateAllele(0).toString().charAt(0);
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Pair<Integer, Integer> depth = new Pair<Integer, Integer>(0, 0);
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for ( String sample : stratifiedContexts.keySet() ) {
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//Pair<Integer,Integer> sampleDepth = getSecondaryPileupNonrefCount(ref.getBase(),stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getPileup(), alternate);
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Pair<Integer, Integer> sampleDepth = getSecondaryPileupNonrefCount(ref.getBaseAsChar(), stratifiedContexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).getBasePileup(), alternate);
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depth.first += sampleDepth.first;
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depth.second += sampleDepth.second;
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}
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if ( depth.first == 0 )
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return null;
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double biasedProportion = (1.0 + depth.second) / (1.0 + depth.first);
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double p_transformed = transform(biasedProportion, depth.first+1);
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double expected_transformed = transform(proportionExpectations[0], depth.first+1);
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double chi_square = Math.signum(biasedProportion - proportionExpectations[0])*Math.min(Math.pow(p_transformed - expected_transformed, 2), Double.MAX_VALUE);
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return String.format("%f", chi_square);
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}
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private double transform( double proportion, int depth ) {
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proportion = proportion - epsilon;
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return proportion / ( Math.sqrt ( proportion*(1-proportion)/depth ) );
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}
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private Pair<Integer, Integer> getSecondaryPileupNonrefCount(char ref, ReadBackedPileup p, char snp ) {
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int variantDepth = 0;
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int variantsWithRefSecondBase = 0;
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for (PileupElement pile : p ) {
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byte pbase = pile.getBase();
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byte sbase = pile.getSecondBase();
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if ( BaseUtils.isRegularBase((char)sbase) && BaseUtils.basesAreEqual(pbase, (byte) snp) ) {
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variantDepth++;
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if ( BaseUtils.basesAreEqual(sbase, (byte)ref) ) {
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variantsWithRefSecondBase++;
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}
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}
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}
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return new Pair<Integer, Integer>(variantDepth, variantsWithRefSecondBase);
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}
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}
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