Adding UGCalcLikelihoods and UGCallVariants so that GSA members can break up the calling process into separate steps (calculate the GLs and then call off of those) - useful for Chris's new batch merger. As the docs say, these are absolutely not supported or recommended for public use.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4764 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
ebanks
parent
b4ef716aaf
commit
0d1c905df3
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@ -88,23 +88,6 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
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logYMatrix[0][0] = 0.0;
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logYMatrix[0][0] = 0.0;
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int j=0;
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int j=0;
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// call clear ref sites separately to speed computation
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/*
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boolean isClearRefSite = true;
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int bestAFguess = 0;
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for ( String sample : GLs.keySet() ) {
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double[] genotypeLikelihoods = GLs.get(sample).getLikelihoods();
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if (!(genotypeLikelihoods[0] > genotypeLikelihoods[1] &&
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genotypeLikelihoods[0] > genotypeLikelihoods[2]))
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isClearRefSite = false;
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bestAFguess += MathUtils.maxElementIndex(genotypeLikelihoods);
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}
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*/
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for ( Map.Entry<String, Genotype> sample : GLs.entrySet() ) {
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for ( Map.Entry<String, Genotype> sample : GLs.entrySet() ) {
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j++;
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j++;
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@ -121,9 +104,6 @@ public class ExactAFCalculationModel extends AlleleFrequencyCalculationModel {
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logYMatrix[j][0] = logYMatrix[j-1][0] + genotypeLikelihoods[GenotypeType.AA.ordinal()];
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logYMatrix[j][0] = logYMatrix[j-1][0] + genotypeLikelihoods[GenotypeType.AA.ordinal()];
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for (int k=1; k <= 2*j; k++ ) {
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for (int k=1; k <= 2*j; k++ ) {
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// if (k > 3 && isClearRefSite)
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// break;
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//double num = (2.0*j-k)*(2.0*j-k-1)*YMatrix[j-1][k] * genotypeLikelihoods[GenotypeType.AA.ordinal()];
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//double num = (2.0*j-k)*(2.0*j-k-1)*YMatrix[j-1][k] * genotypeLikelihoods[GenotypeType.AA.ordinal()];
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double logNumerator[];
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double logNumerator[];
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@ -0,0 +1,112 @@
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/*
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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.genotyper;
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import org.broad.tribble.vcf.*;
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import org.broadinstitute.sting.commandline.ArgumentCollection;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.gatk.DownsampleType;
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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.*;
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import org.broadinstitute.sting.utils.SampleUtils;
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import java.util.*;
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/**
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* Uses the UG engine to determine per-sample genotype likelihoods and emits them as a VCF (using PLs).
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* Absolutely not supported or recommended for public use.
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*/
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@Reference(window=@Window(start=-200,stop=200))
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@By(DataSource.READS)
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@Downsample(by=DownsampleType.BY_SAMPLE, toCoverage=250)
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public class UGCalcLikelihoods extends LocusWalker<VariantCallContext, Integer> implements TreeReducible<Integer> {
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@ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
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// control the output
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@Output(doc="File to which variants should be written",required=true)
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protected VCFWriter writer = null;
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// the calculation arguments
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private UnifiedGenotyperEngine UG_engine = null;
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// enable deletions in the pileup
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public boolean includeReadsWithDeletionAtLoci() { return true; }
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// enable extended events for indels
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public boolean generateExtendedEvents() { return UAC.GLmodel == GenotypeLikelihoodsCalculationModel.Model.DINDEL; }
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public void initialize() {
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// get all of the unique sample names
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// if we're supposed to assume a single sample, do so
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Set<String> samples = new TreeSet<String>();
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if ( UAC.ASSUME_SINGLE_SAMPLE != null )
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samples.add(UAC.ASSUME_SINGLE_SAMPLE);
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else
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samples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
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UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples);
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// initialize the header
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Set<VCFHeaderLine> headerInfo = new HashSet<VCFHeaderLine>();
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headerInfo.add(new VCFInfoHeaderLine(VCFConstants.DOWNSAMPLED_KEY, 0, VCFHeaderLineType.Flag, "Were any of the samples downsampled?"));
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headerInfo.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
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headerInfo.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
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headerInfo.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, 3, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic"));
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writer.writeHeader(new VCFHeader(headerInfo, samples)) ;
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}
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public VariantCallContext map(RefMetaDataTracker tracker, ReferenceContext refContext, AlignmentContext rawContext) {
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return new VariantCallContext(UG_engine.calculateLikelihoods(tracker, refContext, rawContext), refContext.getBase(), true);
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}
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public Integer reduceInit() { return 0; }
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public Integer treeReduce(Integer lhs, Integer rhs) {
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return lhs + rhs;
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}
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public Integer reduce(VariantCallContext value, Integer sum) {
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if ( value == null )
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return sum;
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try {
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writer.add(value.vc, value.refBase);
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} catch (IllegalArgumentException e) {
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throw new IllegalArgumentException(e.getMessage() + "; this is often caused by using the --assume_single_sample_reads argument with the wrong sample name");
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}
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return sum + 1;
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}
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public void onTraversalDone(Integer sum) {
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logger.info(String.format("Visited bases: %d", sum));
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}
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}
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@ -0,0 +1,152 @@
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/*
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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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* 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.genotyper;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.vcf.*;
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import org.broadinstitute.sting.commandline.ArgumentCollection;
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import org.broadinstitute.sting.commandline.Output;
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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.contexts.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.gatk.datasources.simpleDataSources.ReferenceOrderedDataSource;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import java.util.*;
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/**
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* Uses the UG engine to call variants based off of VCFs annotated with GLs (or PLs).
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* Absolutely not supported or recommended for public use.
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*/
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public class UGCallVariants extends RodWalker<VariantCallContext, Integer> {
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@ArgumentCollection
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private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
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// control the output
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@Output(doc="File to which variants should be written",required=true)
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protected VCFWriter writer = null;
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// the calculation arguments
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private UnifiedGenotyperEngine UG_engine = null;
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// variant track names
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private Set<String> trackNames = new HashSet<String>();
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public void initialize() {
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UAC.NO_SLOD = true;
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for ( ReferenceOrderedDataSource d : getToolkit().getRodDataSources() ) {
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if ( d.getName().startsWith("variant") )
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trackNames.add(d.getName());
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}
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if ( trackNames.size() == 0 )
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throw new UserException("At least one track bound to a name beginning with 'variant' must be provided.");
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Set<String> samples = SampleUtils.getSampleListWithVCFHeader(getToolkit(), trackNames);
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UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, samples);
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Set<VCFHeaderLine> headerInfo = new HashSet<VCFHeaderLine>();
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headerInfo.add(new VCFInfoHeaderLine(VCFConstants.ALLELE_FREQUENCY_KEY, -1, VCFHeaderLineType.Float, "Allele Frequency, for each ALT allele, in the same order as listed"));
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headerInfo.add(new VCFInfoHeaderLine(VCFConstants.ALLELE_COUNT_KEY, -1, VCFHeaderLineType.Integer, "Allele count in genotypes, for each ALT allele, in the same order as listed"));
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headerInfo.add(new VCFInfoHeaderLine(VCFConstants.ALLELE_NUMBER_KEY, 1, VCFHeaderLineType.Integer, "Total number of alleles in called genotypes"));
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headerInfo.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_KEY, 1, VCFHeaderLineType.String, "Genotype"));
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headerInfo.add(new VCFFormatHeaderLine(VCFConstants.GENOTYPE_QUALITY_KEY, 1, VCFHeaderLineType.Float, "Genotype Quality"));
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headerInfo.add(new VCFFormatHeaderLine(VCFConstants.DEPTH_KEY, 1, VCFHeaderLineType.Integer, "Read Depth (only filtered reads used for calling)"));
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headerInfo.add(new VCFFormatHeaderLine(VCFConstants.PHRED_GENOTYPE_LIKELIHOODS_KEY, 3, VCFHeaderLineType.Float, "Normalized, Phred-scaled likelihoods for AA,AB,BB genotypes where A=ref and B=alt; not applicable if site is not biallelic"));
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if ( UAC.STANDARD_CONFIDENCE_FOR_EMITTING < UAC.STANDARD_CONFIDENCE_FOR_CALLING ||
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UAC.TRIGGER_CONFIDENCE_FOR_EMITTING < UAC.TRIGGER_CONFIDENCE_FOR_CALLING )
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headerInfo.add(new VCFFilterHeaderLine(UnifiedGenotyperEngine.LOW_QUAL_FILTER_NAME, "Low quality"));
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// initialize the header
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writer.writeHeader(new VCFHeader(headerInfo, samples));
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}
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public VariantCallContext map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null )
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return null;
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List<VariantContext> VCs = new ArrayList<VariantContext>();
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for ( String name : trackNames ) {
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Collection<VariantContext> vc = tracker.getVariantContexts(ref, name, null, context.getLocation(), true, true);
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VCs.addAll(vc);
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}
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VariantContext mergedVC = mergeVCsWithGLs(VCs);
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if ( mergedVC == null )
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return null;
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return UG_engine.calculateGenotypes(tracker, ref, context, mergedVC);
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}
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public Integer reduceInit() { return 0; }
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public Integer reduce(VariantCallContext value, Integer sum) {
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if ( value == null || value.vc == null )
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return sum;
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try {
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Map<String, Object> attrs = new HashMap<String, Object>(value.vc.getAttributes());
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VariantContextUtils.calculateChromosomeCounts(value.vc, attrs, true);
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writer.add(VariantContext.modifyAttributes(value.vc, attrs), value.refBase);
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} catch (IllegalArgumentException e) {
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throw new IllegalArgumentException(e.getMessage() + "; this is often caused by using the --assume_single_sample_reads argument with the wrong sample name");
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}
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return sum + 1;
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}
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public void onTraversalDone(Integer result) {
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logger.info(String.format("Visited sites: %d", result));
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}
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private static VariantContext mergeVCsWithGLs(List<VariantContext> VCs) {
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// we can't use the VCUtils classes because our VCs can all be no-calls
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if ( VCs.size() == 0 )
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return null;
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VariantContext vc = VCs.get(0);
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Map<String, Genotype> genotypes = new HashMap<String, Genotype>(getGenotypesWithGLs(vc.getGenotypes()));
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for (int i = 1; i < VCs.size(); i++)
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genotypes.putAll(getGenotypesWithGLs(VCs.get(i).getGenotypes()));
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return new VariantContext("VCwithGLs", vc.getChr(), vc.getStart(), vc.getEnd(), vc.getAlleles(), genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, null);
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}
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private static Map<String, Genotype> getGenotypesWithGLs(Map<String, Genotype> genotypes) {
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Map<String, Genotype> genotypesWithGLs = new HashMap<String, Genotype>();
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for ( Map.Entry<String, Genotype> g : genotypes.entrySet() ) {
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if ( g.getValue().hasLikelihoods() && g.getValue().getLikelihoods().getAsVector() != null )
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genotypesWithGLs.put(g.getKey(), g.getValue());
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}
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return genotypesWithGLs;
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}
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}
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@ -448,6 +448,8 @@ public class UnifiedGenotyperEngine {
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}
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}
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private VariantCallContext estimateReferenceConfidence(Map<String, StratifiedAlignmentContext> contexts, double theta, boolean ignoreCoveredSamples, double initialPofRef) {
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private VariantCallContext estimateReferenceConfidence(Map<String, StratifiedAlignmentContext> contexts, double theta, boolean ignoreCoveredSamples, double initialPofRef) {
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if ( contexts == null )
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return null;
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double P_of_ref = initialPofRef;
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double P_of_ref = initialPofRef;
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