Initial version of multi-allelic summary module in VariantEval
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Eric Banks
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/*
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* Copyright (c) 2011, 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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* 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 THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
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import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.interval.IntervalUtils;
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import org.broadinstitute.sting.utils.variantcontext.*;
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import java.util.*;
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@Analysis(description = "Evaluation summary for multi-allelic variants")
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public class MultiallelicSummary extends VariantEvaluator implements StandardEval {
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final protected static Logger logger = Logger.getLogger(MultiallelicSummary.class);
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public enum Type {
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SNP, INDEL
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}
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// basic counts on various rates found
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@DataPoint(description = "Number of processed loci")
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public long nProcessedLoci = 0;
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@DataPoint(description = "Number of SNPs")
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public int nSNPs = 0;
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@DataPoint(description = "Number of multi-allelic SNPs")
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public int nMultiSNPs = 0;
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@DataPoint(description = "% processed sites that are multi-allelic SNPs", format = "%.5f")
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public double processedMultiSnpRatio = 0;
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@DataPoint(description = "% SNP sites that are multi-allelic", format = "%.3f")
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public double variantMultiSnpRatio = 0;
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@DataPoint(description = "Number of Indels")
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public int nIndels = 0;
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@DataPoint(description = "Number of multi-allelic Indels")
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public int nMultiIndels = 0;
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@DataPoint(description = "% processed sites that are multi-allelic Indels", format = "%.5f")
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public double processedMultiIndelRatio = 0;
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@DataPoint(description = "% Indel sites that are multi-allelic", format = "%.3f")
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public double variantMultiIndelRatio = 0;
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@DataPoint(description = "Number of Transitions")
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public int nTi = 0;
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@DataPoint(description = "Number of Transversions")
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public int nTv = 0;
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@DataPoint(description = "Overall TiTv ratio", format = "%.2f")
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public double TiTvRatio = 0;
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@DataPoint(description = "Multi-allelic SNPs partially known")
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public int knownSNPsPartial = 0;
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@DataPoint(description = "Multi-allelic SNPs completely known")
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public int knownSNPsComplete = 0;
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@DataPoint(description = "Multi-allelic SNP Novelty Rate")
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public String SNPNoveltyRate = "NA";
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@DataPoint(description = "Multi-allelic Indels partially known")
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public int knownIndelsPartial = 0;
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@DataPoint(description = "Multi-allelic Indels completely known")
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public int knownIndelsComplete = 0;
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@DataPoint(description = "Multi-allelic Indel Novelty Rate")
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public String indelNoveltyRate = "NA";
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// TODO -- Also, AF distributions (pairwise like TiTv)
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public void initialize(VariantEvalWalker walker) {}
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@Override public boolean enabled() { return true; }
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public int getComparisonOrder() {
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return 2;
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}
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public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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nProcessedLoci += context.getSkippedBases() + (ref == null ? 0 : 1);
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}
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public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( eval == null || eval.isMonomorphicInSamples() )
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return null;
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// update counts
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switch ( eval.getType() ) {
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case SNP:
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nSNPs++;
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if ( !eval.isBiallelic() ) {
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nMultiSNPs++;
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calculatePairwiseTiTv(eval);
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calculateSNPPairwiseNovelty(eval, comp);
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}
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break;
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case INDEL:
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nIndels++;
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if ( !eval.isBiallelic() ) {
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nMultiIndels++;
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calculateIndelPairwiseNovelty(eval, comp);
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}
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break;
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default:
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throw new UserException.BadInput("Unexpected variant context type: " + eval);
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}
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return null; // we don't capture any interesting sites
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}
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private void calculatePairwiseTiTv(VariantContext vc) {
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for ( Allele alt : vc.getAlternateAlleles() ) {
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if ( VariantContextUtils.isTransition(vc.getReference(), alt) )
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nTi++;
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else
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nTv++;
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}
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}
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private void calculateSNPPairwiseNovelty(VariantContext eval, VariantContext comp) {
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if ( comp == null )
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return;
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int knownAlleles = 0;
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for ( Allele alt : eval.getAlternateAlleles() ) {
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if ( comp.getAlternateAlleles().contains(alt) )
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knownAlleles++;
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}
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if ( knownAlleles == eval.getAlternateAlleles().size() )
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knownSNPsComplete++;
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else if ( knownAlleles > 0 )
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knownSNPsPartial++;
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}
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private void calculateIndelPairwiseNovelty(VariantContext eval, VariantContext comp) {
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}
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private final String noveltyRate(final int all, final int known) {
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final int novel = all - known;
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final double rate = (novel / (1.0 * all));
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return all == 0 ? "NA" : String.format("%.2f", rate);
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}
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public void finalizeEvaluation() {
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processedMultiSnpRatio = (double)nMultiSNPs / (double)nProcessedLoci;
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variantMultiSnpRatio = (double)nMultiSNPs / (double)nSNPs;
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processedMultiIndelRatio = (double)nMultiIndels / (double)nProcessedLoci;
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variantMultiIndelRatio = (double)nMultiIndels / (double)nIndels;
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TiTvRatio = (double)nTi / (double)nTv;
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SNPNoveltyRate = noveltyRate(nMultiSNPs, knownSNPsPartial + knownSNPsComplete);
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indelNoveltyRate = noveltyRate(nMultiSNPs, knownIndelsPartial + knownIndelsComplete);
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}
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}
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@ -1073,6 +1073,14 @@ public class VariantContextUtils {
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return getSNPSubstitutionType(context) == BaseUtils.BaseSubstitutionType.TRANSVERSION;
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}
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public static boolean isTransition(Allele ref, Allele alt) {
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return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSITION;
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}
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public static boolean isTransversion(Allele ref, Allele alt) {
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return BaseUtils.SNPSubstitutionType(ref.getBases()[0], alt.getBases()[0]) == BaseUtils.BaseSubstitutionType.TRANSVERSION;
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}
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/**
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* create a genome location, given a variant context
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* @param genomeLocParser parser
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