QSample walker for 1KG -- measures aggregate quality of sequencing. Includes misc. improvements throughtout the code, including using the new Tribble GenotypeLikelihoods class for working with VCF GLs from the UG
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4211 348d0f76-0448-11de-a6fe-93d51630548a
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@ -146,6 +146,7 @@ public class DiploidGenotypeCalculationModel extends JointEstimateGenotypeCalcul
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HashMap<String, Object> attributes = new HashMap<String, Object>();
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attributes.put(VCFConstants.DEPTH_KEY, contexts.get(sample).getContext(StratifiedAlignmentContext.StratifiedContextType.COMPLETE).size());
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// todo -- replace with GenotypeLikelihoods object in Tribble library
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double[] likelihoods = GLs.get(sample).getLikelihoods();
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String GL = String.format("%.2f,%.2f,%.2f",
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likelihoods[refGenotype.ordinal()],
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@ -0,0 +1,166 @@
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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.playground.gatk.walkers;
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import net.sf.samtools.SAMReadGroupRecord;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.variantcontext.GenotypeLikelihoods;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.vcf.VCFHeader;
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import org.broadinstitute.sting.commandline.Argument;
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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.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.*;
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import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
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import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
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import org.broadinstitute.sting.gatk.walkers.genotyper.VariantCallContext;
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import org.broadinstitute.sting.utils.MathUtils;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.genotype.DiploidGenotype;
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import org.broadinstitute.sting.utils.vcf.VCFUtils;
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import java.io.PrintStream;
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import java.util.*;
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/**
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* A walker that merges multiple batches of calls, by calling into the Genotyper to fill in sites that
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* were called in one batch but not another.
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*/
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//@Reference(window=@Window(start=-20,stop=20))
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@By(DataSource.REFERENCE)
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@Allows(value={DataSource.READS, DataSource.REFERENCE})
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//@Requires(value={},referenceMetaData=@RMD(name="genotypes", type=VariantContext.class))
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public class QSampleWalker extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
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@ArgumentCollection private UnifiedArgumentCollection UAC = new UnifiedArgumentCollection();
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@Argument(shortName = "E", doc="If true, all sites will have pHet emitted into output file")
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boolean SHOW_EACH_SITE;
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@Output(doc = "QSample Log File", required = true)
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public PrintStream out;
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Map<String, ArrayList<Double>> qSampleScores = new HashMap<String, ArrayList<Double>>();
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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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Set<String> samples;
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public void initialize() {
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Map<String, VCFHeader> headers = VCFUtils.getVCFHeadersFromRods(getToolkit(), Arrays.asList("genotypes"));
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for ( String sample : SampleUtils.getSampleList(headers) ) {
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qSampleScores.put(sample, new ArrayList<Double>());
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}
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// update the engine
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UG_engine = new UnifiedGenotyperEngine(getToolkit(), UAC, logger, null, null, null);
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Set<String> bamSamples = SampleUtils.getSAMFileSamples(getToolkit().getSAMFileHeader());
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Set<String> rodSamples = qSampleScores.keySet();
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samples = new LinkedHashSet<String>(bamSamples);
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samples.retainAll(rodSamples);
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logger.info("# bam samples : " + bamSamples);
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logger.info("# rod samples : " + rodSamples);
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logger.info("# common samples : " + samples);
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for ( String sample : samples ) {
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out.print(sample);
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out.print("\t");
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}
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out.println();
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null )
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return 0;
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// get the calls at this locus
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VariantContext genotypesVC = tracker.getVariantContext(ref, "genotypes", null, context.getLocation(), true);
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if ( genotypesVC == null )
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return 0; // protect ourselves for runs with BTI
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VariantCallContext vcc = UG_engine.runGenotyper(tracker, ref, context);
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logger.info(String.format("Visiting site %s", context.getLocation()));
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for ( String sample : samples ) {
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Genotype g = genotypesVC.getGenotype(sample);
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double pHet = -1;
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if ( g.isHet() ) {
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pHet = scoreSample(sample, vcc);
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qSampleScores.get(sample).add(pHet);
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//logger.info(String.format(" het sample %s with score %.3f", sample, pHet));
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}
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if ( SHOW_EACH_SITE ) out.printf("%s\t", pHet == -1 ? "NA" : String.format("%.3f", pHet));
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}
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if ( SHOW_EACH_SITE ) out.println();
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return 1;
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}
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private static int HET_INDEX = 1;
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private double scoreSample(String sample, VariantCallContext vcc) {
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if ( vcc == null || vcc.vc == null || vcc.vc.getGenotype(sample) == null )
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return 0.0;
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else {
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// get GLs
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GenotypeLikelihoods gl = vcc.vc.getGenotype(sample).getLikelihoods();
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double[] log10gl = gl.getAsVector();
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return Math.pow(10, log10gl[HET_INDEX]) / MathUtils.sumLog10(log10gl);
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}
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}
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public Integer reduceInit() { return 0; }
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public Integer reduce(Integer value, Integer sum) {
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return value + sum;
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}
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public Integer treeReduce(Integer value, Integer sum) {
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return value + sum;
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}
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public void onTraversalDone(Integer sum) {
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// print out summary statistics
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for ( String sample : samples ) {
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ArrayList<Double> scores = qSampleScores.get(sample);
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double qSample = MathUtils.averageDouble(scores);
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out.printf("%.3f\t", qSample);
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}
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out.println();
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}
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}
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@ -58,6 +58,12 @@ public class MathUtils {
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return s;
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}
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public static double sum(List<Double> values) {
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double s = 0.0;
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for ( double v : values) s += v;
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return s;
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}
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public static double sumLog10(double[] log10values) {
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double s = 0.0;
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for ( double v : log10values) s += Math.pow(10.0, v);
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@ -1,14 +0,0 @@
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package org.broadinstitute.sting.utils.genotype.vcf;
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/**
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* an exception to funnel all parsing exceptions into; this way we can emit the line we choked on as well
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*/
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public class VCFParseException extends RuntimeException {
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public VCFParseException(String message) {
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super(message);
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}
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public VCFParseException(String message, Throwable cause) {
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super(message, cause);
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}
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}
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