VariantEval updates
-- Performance optimizations -- Tables now are cleanly formatted (floats are %.2f printed) -- VariantSummary is a standard report now -- Removed CompEvalGenotypes (it didn't do anything) -- Deleted unused classes in GenotypeConcordance -- Updates integration tests as appropriate
This commit is contained in:
Mark DePristo
parent
5a4856b82e
commit
4107636144
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@ -312,16 +312,17 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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String aastr = (ancestralAlignments == null) ? null : new String(ancestralAlignments.getSubsequenceAt(ref.getLocus().getContig(), ref.getLocus().getStart(), ref.getLocus().getStop()).getBases());
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// --------- track --------- sample - VariantContexts -
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HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> evalVCs = variantEvalUtils.bindVariantContexts(tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled, mergeEvals);
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HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> compVCs = variantEvalUtils.bindVariantContexts(tracker, ref, comps, byFilterIsEnabled, false, false, false);
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HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> evalVCs = variantEvalUtils.bindVariantContexts(tracker, ref, evals, byFilterIsEnabled, true, perSampleIsEnabled, mergeEvals);
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HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> compVCs = variantEvalUtils.bindVariantContexts(tracker, ref, comps, byFilterIsEnabled, false, false, false);
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// for each eval track
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for ( final RodBinding<VariantContext> evalRod : evals ) {
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final HashMap<String, Set<VariantContext>> evalSet = evalVCs.containsKey(evalRod) ? evalVCs.get(evalRod) : new HashMap<String, Set<VariantContext>>(0);
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final Map<String, Collection<VariantContext>> emptyEvalMap = Collections.emptyMap();
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final Map<String, Collection<VariantContext>> evalSet = evalVCs.containsKey(evalRod) ? evalVCs.get(evalRod) : emptyEvalMap;
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// for each sample stratifier
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for ( final String sampleName : sampleNamesForStratification ) {
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Set<VariantContext> evalSetBySample = evalSet.get(sampleName);
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Collection<VariantContext> evalSetBySample = evalSet.get(sampleName);
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if ( evalSetBySample == null ) {
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evalSetBySample = new HashSet<VariantContext>(1);
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evalSetBySample.add(null);
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@ -337,8 +338,8 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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// for each comp track
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for ( final RodBinding<VariantContext> compRod : comps ) {
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// no sample stratification for comps
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final HashMap<String, Set<VariantContext>> compSetHash = compVCs.get(compRod);
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final Set<VariantContext> compSet = (compSetHash == null || compSetHash.size() == 0) ? new HashSet<VariantContext>(0) : compVCs.get(compRod).values().iterator().next();
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final HashMap<String, Collection<VariantContext>> compSetHash = compVCs.get(compRod);
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final Collection<VariantContext> compSet = (compSetHash == null || compSetHash.size() == 0) ? Collections.<VariantContext>emptyList() : compVCs.get(compRod).values().iterator().next();
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// find the comp
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final VariantContext comp = findMatchingComp(eval, compSet);
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@ -382,7 +383,7 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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return null;
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}
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private VariantContext findMatchingComp(final VariantContext eval, final Set<VariantContext> comps) {
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private VariantContext findMatchingComp(final VariantContext eval, final Collection<VariantContext> comps) {
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// if no comps, return null
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if ( comps == null || comps.isEmpty() )
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return null;
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@ -447,11 +448,11 @@ public class VariantEvalWalker extends RodWalker<Integer, Integer> implements Tr
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TableType t = (TableType) field.get(ve);
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String subTableName = ve.getClass().getSimpleName() + "." + field.getName();
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String subTableDesc = datamap.get(field).description();
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final DataPoint dataPointAnn = datamap.get(field);
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GATKReportTable table;
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if (!report.hasTable(subTableName)) {
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report.addTable(subTableName, subTableDesc);
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report.addTable(subTableName, dataPointAnn.description());
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table = report.getTable(subTableName);
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table.addPrimaryKey("entry", false);
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@ -1,35 +0,0 @@
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package org.broadinstitute.sting.gatk.walkers.varianteval.evaluators;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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class NewCompEvalGenotypes {
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private GenomeLoc loc;
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private Genotype compGt;
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private Genotype evalGt;
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public NewCompEvalGenotypes(GenomeLoc loc, Genotype compGt, Genotype evalGt) {
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this.loc = loc;
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this.compGt = compGt;
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this.evalGt = evalGt;
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}
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public GenomeLoc getLocus() {
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return loc;
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}
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public Genotype getCompGenotpye() {
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return compGt;
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}
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public Genotype getEvalGenotype() {
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return evalGt;
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}
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public void setCompGenotype(Genotype compGt) {
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this.compGt = compGt;
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}
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public void setEvalGenotype(Genotype evalGt) {
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this.evalGt = evalGt;
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}
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}
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@ -28,13 +28,13 @@ public class CompOverlap extends VariantEvaluator implements StandardEval {
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@DataPoint(description = "number of eval sites at comp sites")
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long nVariantsAtComp = 0;
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@DataPoint(description = "percentage of eval sites at comp sites")
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@DataPoint(description = "percentage of eval sites at comp sites", format = "%.2f" )
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double compRate = 0.0;
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@DataPoint(description = "number of concordant sites")
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long nConcordant = 0;
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@DataPoint(description = "the concordance rate")
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@DataPoint(description = "the concordance rate", format = "%.2f")
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double concordantRate = 0.0;
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public int getComparisonOrder() {
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@ -62,17 +62,17 @@ public class CountVariants extends VariantEvaluator implements StandardEval {
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public long nHomDerived = 0;
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// calculations that get set in the finalizeEvaluation method
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@DataPoint(description = "heterozygosity per locus rate")
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@DataPoint(description = "heterozygosity per locus rate", format = "%.2e")
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public double heterozygosity = 0;
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@DataPoint(description = "heterozygosity per base pair")
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@DataPoint(description = "heterozygosity per base pair", format = "%.2f")
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public double heterozygosityPerBp = 0;
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@DataPoint(description = "heterozygosity to homozygosity ratio")
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@DataPoint(description = "heterozygosity to homozygosity ratio", format = "%.2f")
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public double hetHomRatio = 0;
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@DataPoint(description = "indel rate (insertion count + deletion count)")
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@DataPoint(description = "indel rate (insertion count + deletion count)", format = "%.2e")
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public double indelRate = 0;
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@DataPoint(description = "indel rate per base pair")
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@DataPoint(description = "indel rate per base pair", format = "%.2f")
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public double indelRatePerBp = 0;
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@DataPoint(description = "deletion to insertion ratio")
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@DataPoint(description = "deletion to insertion ratio", format = "%.2f")
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public double deletionInsertionRatio = 0;
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private double perLocusRate(long n) {
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@ -1,159 +0,0 @@
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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.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.exceptions.UserException;
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import org.broadinstitute.sting.utils.variantcontext.Genotype;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.util.EnumMap;
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import java.util.HashMap;
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import java.util.Map;
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@Analysis(description = "Build 1000 Genome Phase I paper summary of variants table")
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public class G1KPhaseITable extends VariantEvaluator {
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// basic counts on various rates found
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@DataPoint(description = "Number of samples")
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public long nSamples = 0;
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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 long nSNPs = 0;
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@DataPoint(description = "SNP Novelty Rate")
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public String SNPNoveltyRate = "NA";
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@DataPoint(description = "Mean number of SNPs per individual")
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public long nSNPsPerSample = 0;
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@DataPoint(description = "Number of Indels")
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public long nIndels = 0;
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@DataPoint(description = "Indel Novelty Rate")
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public String IndelNoveltyRate = "NA";
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@DataPoint(description = "Mean number of Indels per individual")
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public long nIndelsPerSample = 0;
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@DataPoint(description = "Number of SVs")
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public long nSVs = 0;
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@DataPoint(description = "SV Novelty Rate")
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public String SVNoveltyRate = "NA";
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@DataPoint(description = "Mean number of SVs per individual")
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public long nSVsPerSample = 0;
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Map<VariantContext.Type, Integer> allVariantCounts, knownVariantCounts;
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Map<String, Map<VariantContext.Type, Integer>> countsPerSample;
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private final Map<VariantContext.Type, Integer> makeCounts() {
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Map<VariantContext.Type, Integer> counts = new EnumMap<VariantContext.Type, Integer>(VariantContext.Type.class);
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counts.put(VariantContext.Type.SNP, 0);
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counts.put(VariantContext.Type.INDEL, 0);
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counts.put(VariantContext.Type.SYMBOLIC, 0);
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return counts;
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}
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public void initialize(VariantEvalWalker walker) {
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countsPerSample = new HashMap<String, Map<VariantContext.Type, Integer>>();
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nSamples = walker.getSampleNamesForEvaluation().size();
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for ( String sample : walker.getSampleNamesForEvaluation() ) {
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countsPerSample.put(sample, makeCounts());
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}
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allVariantCounts = makeCounts();
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knownVariantCounts = makeCounts();
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}
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@Override public boolean enabled() { return true; }
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public int getComparisonOrder() {
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return 2; // we only need to see each eval track
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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() ) return null;
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switch (eval.getType()) {
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case SNP:
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case INDEL:
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case SYMBOLIC:
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allVariantCounts.put(eval.getType(), allVariantCounts.get(eval.getType()) + 1);
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if ( comp != null )
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knownVariantCounts.put(eval.getType(), knownVariantCounts.get(eval.getType()) + 1);
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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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// count variants per sample
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for (final Genotype g : eval.getGenotypes()) {
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if ( ! g.isNoCall() && ! g.isHomRef() ) {
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int count = countsPerSample.get(g.getSampleName()).get(eval.getType());
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countsPerSample.get(g.getSampleName()).put(eval.getType(), count + 1);
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}
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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 final int perSampleMean(VariantContext.Type type) {
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long sum = 0;
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for ( Map<VariantContext.Type, Integer> count : countsPerSample.values() ) {
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sum += count.get(type);
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}
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return (int)(Math.round(sum / (1.0 * countsPerSample.size())));
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}
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private final String noveltyRate(VariantContext.Type type) {
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int all = allVariantCounts.get(type);
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int known = knownVariantCounts.get(type);
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int novel = all - known;
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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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nSNPs = allVariantCounts.get(VariantContext.Type.SNP);
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nIndels = allVariantCounts.get(VariantContext.Type.INDEL);
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nSVs = allVariantCounts.get(VariantContext.Type.SYMBOLIC);
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nSNPsPerSample = perSampleMean(VariantContext.Type.SNP);
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nIndelsPerSample = perSampleMean(VariantContext.Type.INDEL);
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nSVsPerSample = perSampleMean(VariantContext.Type.SYMBOLIC);
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SNPNoveltyRate = noveltyRate(VariantContext.Type.SNP);
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IndelNoveltyRate = noveltyRate(VariantContext.Type.INDEL);
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SVNoveltyRate = noveltyRate(VariantContext.Type.SYMBOLIC);
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}
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}
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@ -445,39 +445,6 @@ class SampleStats implements TableType {
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}
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}
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/**
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* Sample stats, but for AC
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*/
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class ACStats extends SampleStats {
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private String[] rowKeys;
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public ACStats(VariantContext evalvc, VariantContext compvc, int nGenotypeTypes) {
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super(nGenotypeTypes);
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rowKeys = new String[1+2*evalvc.getGenotypes().size()+1+2*compvc.getGenotypes().size()];
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for ( int i = 0; i <= 2*evalvc.getGenotypes().size(); i++ ) { // todo -- assuming ploidy 2 here...
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concordanceStats.put(String.format("evalAC%d",i),new long[nGenotypeTypes][nGenotypeTypes]);
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rowKeys[i] = String.format("evalAC%d",i);
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}
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for ( int i = 0; i <= 2*compvc.getGenotypes().size(); i++ ) {
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concordanceStats.put(String.format("compAC%d",i), new long[nGenotypeTypes][nGenotypeTypes]);
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rowKeys[1+2*evalvc.getGenotypes().size()+i] = String.format("compAC%d",i);
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}
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}
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public String getName() {
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return "Allele Count Statistics";
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}
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public Object[] getRowKeys() {
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if ( rowKeys == null ) {
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throw new StingException("RowKeys is null!");
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}
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return rowKeys;
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}
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}
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/**
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* a table of sample names to genotype concordance summary statistics
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*/
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@ -637,79 +604,3 @@ class SampleSummaryStats implements TableType {
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}
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}
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/**
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* SampleSummaryStats .. but for allele counts
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*/
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class ACSummaryStats extends SampleSummaryStats {
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private String[] rowKeys;
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public ACSummaryStats (final VariantContext evalvc, final VariantContext compvc) {
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concordanceSummary.put(ALL_SAMPLES_KEY, new double[COLUMN_KEYS.length]);
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rowKeys = new String[3+2*evalvc.getGenotypes().size() + 2*compvc.getGenotypes().size()];
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rowKeys[0] = ALL_SAMPLES_KEY;
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for( int i = 0; i <= 2*evalvc.getGenotypes().size() ; i ++ ) {
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concordanceSummary.put(String.format("evalAC%d",i), new double[COLUMN_KEYS.length]);
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rowKeys[i+1] = String.format("evalAC%d",i);
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}
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for( int i = 0; i <= 2*compvc.getGenotypes().size() ; i ++ ) {
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concordanceSummary.put(String.format("compAC%d",i), new double[COLUMN_KEYS.length]);
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rowKeys[2+2*evalvc.getGenotypes().size()+i] = String.format("compAC%d",i);
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}
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}
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public String getName() {
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return "Allele Count Summary Statistics";
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}
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public Object[] getRowKeys() {
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if ( rowKeys == null) {
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throw new StingException("rowKeys is null!!");
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}
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return rowKeys;
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}
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}
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class CompACNames implements Comparator{
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final Logger myLogger;
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private boolean info = true;
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public CompACNames(Logger l) {
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myLogger = l;
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}
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public boolean equals(Object o) {
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return ( o.getClass() == CompACNames.class );
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}
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public int compare(Object o1, Object o2) {
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if ( info ) {
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myLogger.info("Sorting AC names");
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info = false;
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}
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//System.out.printf("Objects %s %s get ranks %d %d%n",o1.toString(),o2.toString(),getRank(o1),getRank(o2));
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return getRank(o1) - getRank(o2);
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}
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public int getRank(Object o) {
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if ( o.getClass() != String.class ) {
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return Integer.MIN_VALUE/4;
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} else {
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String s = (String) o;
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if ( s.startsWith("eval") ) {
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return Integer.MIN_VALUE/4 + 1 + parseAC(s);
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} else if ( s.startsWith("comp") ) {
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return 1+ parseAC(s);
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} else {
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return Integer.MIN_VALUE/4;
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}
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}
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}
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public int parseAC(String s) {
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String[] g = s.split("AC");
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return Integer.parseInt(g[1]);
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}
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}
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@ -16,19 +16,19 @@ public class TiTvVariantEvaluator extends VariantEvaluator implements StandardEv
|
|||
long nTi = 0;
|
||||
@DataPoint(description = "number of transversion loci")
|
||||
long nTv = 0;
|
||||
@DataPoint(description = "the transition to transversion ratio")
|
||||
@DataPoint(description = "the transition to transversion ratio", format = "%.2f")
|
||||
double tiTvRatio = 0.0;
|
||||
@DataPoint(description = "number of comp transition sites")
|
||||
long nTiInComp = 0;
|
||||
@DataPoint(description = "number of comp transversion sites")
|
||||
long nTvInComp = 0;
|
||||
@DataPoint(description = "the transition to transversion ratio for comp sites")
|
||||
@DataPoint(description = "the transition to transversion ratio for comp sites", format = "%.2f")
|
||||
double TiTvRatioStandard = 0.0;
|
||||
@DataPoint(description = "number of derived transition loci")
|
||||
long nTiDerived = 0;
|
||||
@DataPoint(description = "number of derived transversion loci")
|
||||
long nTvDerived = 0;
|
||||
@DataPoint(description = "the derived transition to transversion ratio")
|
||||
@DataPoint(description = "the derived transition to transversion ratio", format = "%.2f")
|
||||
double tiTvDerivedRatio = 0.0;
|
||||
|
||||
public boolean enabled() {
|
||||
|
|
|
|||
|
|
@ -30,10 +30,10 @@ public class ValidationReport extends VariantEvaluator implements StandardEval {
|
|||
@DataPoint(description = "FN") int FN = 0;
|
||||
@DataPoint(description = "TN") int TN = 0;
|
||||
|
||||
@DataPoint(description = "Sensitivity") double sensitivity = 0;
|
||||
@DataPoint(description = "Specificity") double specificity = 0;
|
||||
@DataPoint(description = "PPV") double PPV = 0;
|
||||
@DataPoint(description = "FDR") double FDR = 0;
|
||||
@DataPoint(description = "Sensitivity", format = "%.2f") double sensitivity = 0;
|
||||
@DataPoint(description = "Specificity", format = "%.2f") double specificity = 0;
|
||||
@DataPoint(description = "PPV", format = "%.2f") double PPV = 0;
|
||||
@DataPoint(description = "FDR", format = "%.2f") double FDR = 0;
|
||||
|
||||
@DataPoint(description = "CompMonoEvalNoCall") int CompMonoEvalNoCall = 0;
|
||||
@DataPoint(description = "CompMonoEvalFiltered") int CompMonoEvalFiltered = 0;
|
||||
|
|
|
|||
|
|
@ -0,0 +1,223 @@
|
|||
/*
|
||||
* Copyright (c) 2011, 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.varianteval.evaluators;
|
||||
|
||||
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.varianteval.VariantEvalWalker;
|
||||
import org.broadinstitute.sting.gatk.walkers.varianteval.util.Analysis;
|
||||
import org.broadinstitute.sting.gatk.walkers.varianteval.util.DataPoint;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
|
||||
import org.broadinstitute.sting.utils.exceptions.UserException;
|
||||
import org.broadinstitute.sting.utils.variantcontext.Genotype;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContext;
|
||||
import org.broadinstitute.sting.utils.variantcontext.VariantContextUtils;
|
||||
|
||||
import java.util.Collection;
|
||||
import java.util.EnumMap;
|
||||
import java.util.HashMap;
|
||||
import java.util.Map;
|
||||
|
||||
@Analysis(description = "1000 Genomes Phase I summary of variants table")
|
||||
public class VariantSummary extends VariantEvaluator implements StandardEval {
|
||||
// basic counts on various rates found
|
||||
@DataPoint(description = "Number of samples")
|
||||
public long nSamples = 0;
|
||||
|
||||
@DataPoint(description = "Number of processed loci")
|
||||
public long nProcessedLoci = 0;
|
||||
|
||||
@DataPoint(description = "Number of SNPs")
|
||||
public long nSNPs = 0;
|
||||
@DataPoint(description = "Overall TiTv ratio", format = "%.2f")
|
||||
public double TiTvRatio = 0;
|
||||
@DataPoint(description = "SNP Novelty Rate")
|
||||
public String SNPNoveltyRate = "NA";
|
||||
@DataPoint(description = "Mean number of SNPs per individual")
|
||||
public long nSNPsPerSample = 0;
|
||||
@DataPoint(description = "Mean TiTv ratio per individual", format = "%.2f")
|
||||
public double TiTvRatioPerSample = 0;
|
||||
@DataPoint(description = "Mean depth of coverage per sample at SNPs", format = "%.1f")
|
||||
public double SNPDPPerSample = 0;
|
||||
|
||||
@DataPoint(description = "Number of Indels")
|
||||
public long nIndels = 0;
|
||||
@DataPoint(description = "Indel Novelty Rate")
|
||||
public String IndelNoveltyRate = "NA";
|
||||
@DataPoint(description = "Mean number of Indels per individual")
|
||||
public long nIndelsPerSample = 0;
|
||||
@DataPoint(description = "Mean depth of coverage per sample at Indels", format = "%.1f")
|
||||
public double IndelDPPerSample = 0;
|
||||
|
||||
@DataPoint(description = "Number of SVs")
|
||||
public long nSVs = 0;
|
||||
@DataPoint(description = "SV Novelty Rate")
|
||||
public String SVNoveltyRate = "NA";
|
||||
@DataPoint(description = "Mean number of SVs per individual")
|
||||
public long nSVsPerSample = 0;
|
||||
|
||||
TypeSampleMap allVariantCounts, knownVariantCounts;
|
||||
TypeSampleMap countsPerSample;
|
||||
TypeSampleMap transitionsPerSample, transversionsPerSample;
|
||||
TypeSampleMap depthPerSample;
|
||||
|
||||
private final static String ALL = "ALL";
|
||||
|
||||
private class TypeSampleMap extends EnumMap<VariantContext.Type, Map<String, Integer>> {
|
||||
public TypeSampleMap(final Collection<String> samples) {
|
||||
super(VariantContext.Type.class);
|
||||
for ( VariantContext.Type type : VariantContext.Type.values() ) {
|
||||
Map<String, Integer> bySample = new HashMap<String, Integer>(samples.size());
|
||||
for ( final String sample : samples ) {
|
||||
bySample.put(sample, 0);
|
||||
}
|
||||
bySample.put(ALL, 0);
|
||||
this.put(type, bySample);
|
||||
}
|
||||
}
|
||||
|
||||
public final void inc(final VariantContext.Type type, final String sample) {
|
||||
final int count = this.get(type).get(sample);
|
||||
get(type).put(sample, count + 1);
|
||||
}
|
||||
|
||||
public final int all(VariantContext.Type type) {
|
||||
return get(type).get(ALL);
|
||||
}
|
||||
|
||||
public final int meanValue(VariantContext.Type type) {
|
||||
long sum = 0;
|
||||
int n = 0;
|
||||
for ( final Map.Entry<String, Integer> pair : get(type).entrySet() ) {
|
||||
if ( pair.getKey() != ALL) {
|
||||
n++;
|
||||
sum += pair.getValue();
|
||||
}
|
||||
}
|
||||
return (int)(Math.round(sum / (1.0 * n)));
|
||||
}
|
||||
|
||||
public final double ratioValue(VariantContext.Type type, TypeSampleMap denoms, boolean allP) {
|
||||
double sum = 0;
|
||||
int n = 0;
|
||||
for ( final String sample : get(type).keySet() ) {
|
||||
if ( (allP && sample == ALL) || (!allP && sample != ALL) ) {
|
||||
final long num = get(type).get(sample);
|
||||
final long denom = denoms.get(type).get(sample);
|
||||
sum += ratio(num, denom);
|
||||
n++;
|
||||
}
|
||||
}
|
||||
return Math.round(sum / (1.0 * n));
|
||||
}
|
||||
}
|
||||
|
||||
|
||||
public void initialize(VariantEvalWalker walker) {
|
||||
nSamples = walker.getSampleNamesForEvaluation().size();
|
||||
countsPerSample = new TypeSampleMap(walker.getSampleNamesForEvaluation());
|
||||
transitionsPerSample = new TypeSampleMap(walker.getSampleNamesForEvaluation());
|
||||
transversionsPerSample = new TypeSampleMap(walker.getSampleNamesForEvaluation());
|
||||
allVariantCounts = new TypeSampleMap(walker.getSampleNamesForEvaluation());
|
||||
knownVariantCounts = new TypeSampleMap(walker.getSampleNamesForEvaluation());
|
||||
depthPerSample = new TypeSampleMap(walker.getSampleNamesForEvaluation());
|
||||
}
|
||||
|
||||
@Override public boolean enabled() { return true; }
|
||||
|
||||
public int getComparisonOrder() {
|
||||
return 2; // we only need to see each eval track
|
||||
}
|
||||
|
||||
public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
nProcessedLoci += context.getSkippedBases() + (ref == null ? 0 : 1);
|
||||
}
|
||||
|
||||
public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
if ( eval == null || eval.isMonomorphicInSamples() ) return null;
|
||||
|
||||
TypeSampleMap titvTable = null;
|
||||
|
||||
switch (eval.getType()) {
|
||||
case SNP:
|
||||
titvTable = VariantContextUtils.isTransition(eval) ? transitionsPerSample : transversionsPerSample;
|
||||
titvTable.inc(eval.getType(), ALL);
|
||||
case INDEL:
|
||||
case SYMBOLIC:
|
||||
allVariantCounts.inc(eval.getType(), ALL);
|
||||
if ( comp != null )
|
||||
knownVariantCounts.inc(eval.getType(), ALL);
|
||||
if ( eval.hasAttribute(VCFConstants.DEPTH_KEY) )
|
||||
depthPerSample.inc(eval.getType(), ALL);
|
||||
break;
|
||||
default:
|
||||
throw new UserException.BadInput("Unexpected variant context type: " + eval);
|
||||
}
|
||||
|
||||
// per sample metrics
|
||||
for (final Genotype g : eval.getGenotypes()) {
|
||||
if ( ! g.isNoCall() && ! g.isHomRef() ) {
|
||||
countsPerSample.inc(eval.getType(), g.getSampleName());
|
||||
|
||||
// update transition / transversion ratio
|
||||
if ( titvTable != null ) titvTable.inc(eval.getType(), g.getSampleName());
|
||||
|
||||
if ( g.hasAttribute(VCFConstants.DEPTH_KEY) )
|
||||
depthPerSample.inc(eval.getType(), g.getSampleName());
|
||||
}
|
||||
}
|
||||
|
||||
return null; // we don't capture any interesting sites
|
||||
}
|
||||
|
||||
private final String noveltyRate(VariantContext.Type type) {
|
||||
final int all = allVariantCounts.all(type);
|
||||
final int known = knownVariantCounts.all(type);
|
||||
final int novel = all - known;
|
||||
final double rate = (novel / (1.0 * all));
|
||||
return all == 0 ? "NA" : String.format("%.2f", rate);
|
||||
}
|
||||
|
||||
public void finalizeEvaluation() {
|
||||
nSNPs = allVariantCounts.all(VariantContext.Type.SNP);
|
||||
nIndels = allVariantCounts.all(VariantContext.Type.INDEL);
|
||||
nSVs = allVariantCounts.all(VariantContext.Type.SYMBOLIC);
|
||||
|
||||
TiTvRatio = transitionsPerSample.ratioValue(VariantContext.Type.SNP, transversionsPerSample, true);
|
||||
TiTvRatioPerSample = transitionsPerSample.ratioValue(VariantContext.Type.SNP, transversionsPerSample, false);
|
||||
|
||||
nSNPsPerSample = countsPerSample.meanValue(VariantContext.Type.SNP);
|
||||
nIndelsPerSample = countsPerSample.meanValue(VariantContext.Type.INDEL);
|
||||
nSVsPerSample = countsPerSample.meanValue(VariantContext.Type.SYMBOLIC);
|
||||
|
||||
SNPNoveltyRate = noveltyRate(VariantContext.Type.SNP);
|
||||
IndelNoveltyRate = noveltyRate(VariantContext.Type.INDEL);
|
||||
SVNoveltyRate = noveltyRate(VariantContext.Type.SYMBOLIC);
|
||||
|
||||
SNPDPPerSample = depthPerSample.meanValue(VariantContext.Type.SNP);
|
||||
IndelDPPerSample = depthPerSample.meanValue(VariantContext.Type.INDEL);
|
||||
}
|
||||
}
|
||||
|
|
@ -6,4 +6,5 @@ import java.lang.annotation.RetentionPolicy;
|
|||
@Retention(RetentionPolicy.RUNTIME)
|
||||
public @interface DataPoint {
|
||||
String description() default ""; // the description, optional
|
||||
String format() default "";
|
||||
}
|
||||
|
|
|
|||
|
|
@ -246,7 +246,7 @@ public class VariantEvalUtils {
|
|||
field.setAccessible(true);
|
||||
|
||||
if (!(field.get(vei) instanceof TableType)) {
|
||||
table.addColumn(field.getName(), 0.0);
|
||||
table.addColumn(field.getName(), 0.0, datamap.get(field).format());
|
||||
}
|
||||
}
|
||||
} catch (InstantiationException e) {
|
||||
|
|
@ -297,6 +297,7 @@ public class VariantEvalUtils {
|
|||
* Additional variant contexts per sample are automatically generated and added to the map unless the sample name
|
||||
* matches the ALL_SAMPLE_NAME constant.
|
||||
*
|
||||
*
|
||||
* @param tracker the metadata tracker
|
||||
* @param ref the reference context
|
||||
* @param tracks the list of tracks to process
|
||||
|
|
@ -308,7 +309,7 @@ public class VariantEvalUtils {
|
|||
*
|
||||
* @return the mapping of track to VC list that should be populated
|
||||
*/
|
||||
public HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>>
|
||||
public HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>>
|
||||
bindVariantContexts(RefMetaDataTracker tracker,
|
||||
ReferenceContext ref,
|
||||
List<RodBinding<VariantContext>> tracks,
|
||||
|
|
@ -319,11 +320,11 @@ public class VariantEvalUtils {
|
|||
if ( tracker == null )
|
||||
return null;
|
||||
|
||||
HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>> bindings = new HashMap<RodBinding<VariantContext>, HashMap<String, Set<VariantContext>>>();
|
||||
HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>> bindings = new HashMap<RodBinding<VariantContext>, HashMap<String, Collection<VariantContext>>>();
|
||||
|
||||
RodBinding<VariantContext> firstTrack = tracks.isEmpty() ? null : tracks.get(0);
|
||||
for ( RodBinding<VariantContext> track : tracks ) {
|
||||
HashMap<String, Set<VariantContext>> mapping = new HashMap<String, Set<VariantContext>>();
|
||||
HashMap<String, Collection<VariantContext>> mapping = new HashMap<String, Collection<VariantContext>>();
|
||||
|
||||
for ( VariantContext vc : tracker.getValues(track, ref.getLocus()) ) {
|
||||
|
||||
|
|
@ -352,9 +353,9 @@ public class VariantEvalUtils {
|
|||
|
||||
if ( mergeTracks && bindings.containsKey(firstTrack) ) {
|
||||
// go through each binding of sample -> value and add all of the bindings from this entry
|
||||
HashMap<String, Set<VariantContext>> firstMapping = bindings.get(firstTrack);
|
||||
for ( Map.Entry<String, Set<VariantContext>> elt : mapping.entrySet() ) {
|
||||
Set<VariantContext> firstMappingSet = firstMapping.get(elt.getKey());
|
||||
HashMap<String, Collection<VariantContext>> firstMapping = bindings.get(firstTrack);
|
||||
for ( Map.Entry<String, Collection<VariantContext>> elt : mapping.entrySet() ) {
|
||||
Collection<VariantContext> firstMappingSet = firstMapping.get(elt.getKey());
|
||||
if ( firstMappingSet != null ) {
|
||||
firstMappingSet.addAll(elt.getValue());
|
||||
} else {
|
||||
|
|
@ -369,9 +370,9 @@ public class VariantEvalUtils {
|
|||
return bindings;
|
||||
}
|
||||
|
||||
private void addMapping(HashMap<String, Set<VariantContext>> mappings, String sample, VariantContext vc) {
|
||||
private void addMapping(HashMap<String, Collection<VariantContext>> mappings, String sample, VariantContext vc) {
|
||||
if ( !mappings.containsKey(sample) )
|
||||
mappings.put(sample, new LinkedHashSet<VariantContext>());
|
||||
mappings.put(sample, new ArrayList<VariantContext>(1));
|
||||
mappings.get(sample).add(vc);
|
||||
}
|
||||
|
||||
|
|
|
|||
|
|
@ -30,7 +30,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("a36414421621b377d6146d58d2fcecd0")
|
||||
Arrays.asList("abe943d1aac120d7e75b9b9e5dac2399")
|
||||
);
|
||||
executeTest("testFunctionClassWithSnpeff", spec);
|
||||
}
|
||||
|
|
@ -50,7 +50,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("6a71b17c19f5914c277a99f45f5d9c39")
|
||||
Arrays.asList("5fd9624c7a35ffb79d0feb1e233fc757")
|
||||
);
|
||||
executeTest("testStratifySamplesAndExcludeMonomorphicSites", spec);
|
||||
}
|
||||
|
|
@ -70,7 +70,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("fb926edfd3d811e18b33798a43ef4379")
|
||||
Arrays.asList("4a8765cd02d36e63f6d0f0c10a6c674b")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndels", spec);
|
||||
}
|
||||
|
|
@ -91,7 +91,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("26b7d57e3a204ac80a28cb29485b59b7")
|
||||
Arrays.asList("4106ab8f742ad1c3138c29220151503c")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNovelty", spec);
|
||||
}
|
||||
|
|
@ -113,7 +113,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("1df8184062f330bea9da8bacacc5a09d")
|
||||
Arrays.asList("6cee3a8d68307a118944f2df5401ac89")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithNoveltyAndFilter", spec);
|
||||
}
|
||||
|
|
@ -134,7 +134,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("927f26414509db9e7c0a2c067d57c949")
|
||||
Arrays.asList("af5dd27354d5dfd0d2fe03149af09b55")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithCpG", spec);
|
||||
}
|
||||
|
|
@ -155,7 +155,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("e6fddefd95122cabc5a0f0b95bce6d34")
|
||||
Arrays.asList("062a231e203671e19aa9c6507710d762")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithFunctionalClass", spec);
|
||||
}
|
||||
|
|
@ -176,7 +176,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("df10486dae73a9cf8c647964f51ba3e0")
|
||||
Arrays.asList("75abdd2b17c0a5e04814b6969a3d4d7e")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithDegeneracy", spec);
|
||||
}
|
||||
|
|
@ -197,7 +197,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("524adb0b7ff70e227b8803a88f36713e")
|
||||
Arrays.asList("bdbb5f8230a4a193058750c5e506c733")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithSample", spec);
|
||||
}
|
||||
|
|
@ -220,7 +220,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("ef6449789dfc032602458b7c5538a1bc")
|
||||
Arrays.asList("f076120da22930294840fcc396f5f141")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithJexlExpression", spec);
|
||||
}
|
||||
|
|
@ -245,7 +245,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("13b90e94fa82d72bb04a0a5addb27c3f")
|
||||
Arrays.asList("69201f4a2a7a44b38805a4aeeb8830b6")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsSNPsandIndelsWithMultipleJexlExpressions", spec);
|
||||
}
|
||||
|
|
@ -264,7 +264,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("8458b9d7803d75aae551fac7dbd152d6")
|
||||
Arrays.asList("c3bd3cb6cfb21a8c2b4d5f69104bf6c2")
|
||||
);
|
||||
executeTest("testFundamentalsCountVariantsNoCompRod", spec);
|
||||
}
|
||||
|
|
@ -277,7 +277,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" --eval " + validationDataLocation + "yri.trio.gatk_glftrio.intersection.annotated.filtered.chr1.vcf" +
|
||||
" --comp:comp_genotypes,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.head.vcf";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(withSelect(tests, "DP < 50", "DP50") + " " + extraArgs + " -ST CpG -o %s",
|
||||
1, Arrays.asList("b954dee127ec4205ed7d33c91aa3e045"));
|
||||
1, Arrays.asList("861f94e3237d62bd5bc00757319241f7"));
|
||||
executeTestParallel("testSelect1", spec);
|
||||
}
|
||||
|
||||
|
|
@ -294,7 +294,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testCompVsEvalAC() {
|
||||
String extraArgs = "-T VariantEval -R "+b36KGReference+" -o %s -ST CpG -EV GenotypeConcordance --eval:evalYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.ug.very.few.lines.vcf --comp:compYRI,VCF3 " + validationDataLocation + "yri.trio.gatk.fake.genotypes.ac.test.vcf";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("ae0027197547731a9a5c1eec5fbe0221"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("955c33365e017679047fabec0f14d5e0"));
|
||||
executeTestParallel("testCompVsEvalAC",spec);
|
||||
}
|
||||
|
||||
|
|
@ -312,7 +312,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
@Test
|
||||
public void testCompOverlap() {
|
||||
String extraArgs = "-T VariantEval -R " + b37KGReference + " -L " + validationDataLocation + "VariantEval/pacbio.hg19.intervals --comp:comphapmap " + comparisonDataLocation + "Validated/HapMap/3.3/genotypes_r27_nr.b37_fwd.vcf --eval " + validationDataLocation + "VariantEval/pacbio.ts.recalibrated.vcf -noEV -EV CompOverlap -sn NA12878 -noST -ST Novelty -o %s";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("009ecc8376a20dce81ff5299ef6bfecb"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("fb7d989e44bd74c5376cb5732f9f3f64"));
|
||||
executeTestParallel("testCompOverlap",spec);
|
||||
}
|
||||
|
||||
|
|
@ -324,7 +324,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" --dbsnp " + b37dbSNP132 +
|
||||
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
|
||||
" -noST -ST Novelty -o %s";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("835b44fc3004cc975c968c9f92ed25d6"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("da5bcb305c5ef207ce175821efdbdefd"));
|
||||
executeTestParallel("testEvalTrackWithoutGenotypes",spec);
|
||||
}
|
||||
|
||||
|
|
@ -336,7 +336,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" --eval:evalBI " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bi.sites.vcf" +
|
||||
" --eval:evalBC " + validationDataLocation + "VariantEval/ALL.20100201.chr20.bc.sites.vcf" +
|
||||
" -noST -ST Novelty -o %s";
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("f0e003f1293343c3210ae95e8936b19a"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("fde839ece1442388f21a2f0b936756a8"));
|
||||
executeTestParallel("testMultipleEvalTracksWithoutGenotypes",spec);
|
||||
}
|
||||
|
||||
|
|
@ -353,13 +353,13 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
" -noST -noEV -ST Novelty -EV CompOverlap" +
|
||||
" -o %s";
|
||||
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("0b81d97f843ec4a1a4222d1f9949bfca"));
|
||||
WalkerTestSpec spec = new WalkerTestSpec(extraArgs,1,Arrays.asList("1efae6b3b88c752b771e0c8fae24464e"));
|
||||
executeTestParallel("testMultipleCompTracks",spec);
|
||||
}
|
||||
|
||||
@Test
|
||||
public void testPerSampleAndSubsettedSampleHaveSameResults() {
|
||||
String md5 = "7425ca5c439afd7bb33ed5cfea02c2b3";
|
||||
public void testPerSampleAndSubsettedSampleHaveSameResults1() {
|
||||
String md5 = "bc9bcabc3105e2515d9a2d41506d2de1";
|
||||
|
||||
WalkerTestSpec spec = new WalkerTestSpec(
|
||||
buildCommandLine(
|
||||
|
|
@ -414,7 +414,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("924b6123edb9da540d0abc66f6f33e16")
|
||||
Arrays.asList("e53546243250634fc03e83b4e61ec55f")
|
||||
);
|
||||
executeTest("testAlleleCountStrat", spec);
|
||||
}
|
||||
|
|
@ -435,7 +435,7 @@ public class VariantEvalIntegrationTest extends WalkerTest {
|
|||
"-o %s"
|
||||
),
|
||||
1,
|
||||
Arrays.asList("9794e2dba205c6929dc89899fdf0bf6b")
|
||||
Arrays.asList("c8086f0525bc13e666afeb670c2e13ae")
|
||||
);
|
||||
executeTest("testIntervalStrat", spec);
|
||||
}
|
||||
|
|
|
|||
Loading…
Reference in New Issue