Examples of VariantAnnotatorEngine

Examples of org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine

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        final GenomeLocParser genomeLocParser = toolkit.getGenomeLocParser();

        genotypingEngine = new HaplotypeCallerGenotypingEngine( SCAC, samplesList, genomeLocParser, FixedAFCalculatorProvider.createThreadSafeProvider(getToolkit(),SCAC,logger), !doNotRunPhysicalPhasing);
        // initialize the output VCF header
        final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());

        final Set<VCFHeaderLine> headerInfo = new HashSet<>();

        headerInfo.addAll(genotypingEngine.getAppropriateVCFInfoHeaders());
        // all annotation fields from VariantAnnotatorEngine
        headerInfo.addAll(annotationEngine.getVCFAnnotationDescriptions());
        // all callers need to add these standard annotation header lines
        VCFStandardHeaderLines.addStandardInfoLines(headerInfo, true,
                VCFConstants.DOWNSAMPLED_KEY,
                VCFConstants.MLE_ALLELE_COUNT_KEY,
                VCFConstants.MLE_ALLELE_FREQUENCY_KEY);
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Examples of org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine

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        final SampleList samples = new IndexedSampleList(SampleUtils.getSampleList(vcfRods, GATKVariantContextUtils.GenotypeMergeType.REQUIRE_UNIQUE));
        // create the genotyping engine
        genotypingEngine = new UnifiedGenotypingEngine(createUAC(), samples, toolkit.getGenomeLocParser(), GeneralPloidyFailOverAFCalculatorProvider.createThreadSafeProvider(toolkit, genotypeArgs, logger),
                toolkit.getArguments().BAQMode);
        // create the annotation engine
        annotationEngine = new VariantAnnotatorEngine(Arrays.asList("none"), annotationsToUse, Collections.<String>emptyList(), this, toolkit);

        // take care of the VCF headers
        final Set<VCFHeaderLine> headerLines = VCFUtils.smartMergeHeaders(vcfRods.values(), true);
        headerLines.addAll(annotationEngine.getVCFAnnotationDescriptions());
        headerLines.addAll(genotypingEngine.getAppropriateVCFInfoHeaders());
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Examples of org.broadinstitute.gatk.tools.walkers.annotator.VariantAnnotatorEngine

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         // initialize the verbose writer
        if ( verboseWriter != null )
            verboseWriter.println("AFINFO\tLOC\tREF\tALT\tMAF\tF\tAFprior\tMLE\tMAP");

        final VariantAnnotatorEngine annotationEngine = new VariantAnnotatorEngine(Arrays.asList(annotationClassesToUse), annotationsToUse, annotationsToExclude, this, getToolkit());

        final AFCalculatorProvider afCalcAFCalculatorProvider = FixedAFCalculatorProvider.createThreadSafeProvider(getToolkit(),UAC,logger);
        genotypingEngine = new UnifiedGenotypingEngine(UAC, samples, toolkit.getGenomeLocParser(), afCalcAFCalculatorProvider, toolkit.getArguments().BAQMode);
        genotypingEngine.setVerboseWriter(verboseWriter);
        genotypingEngine.setAnnotationEngine(annotationEngine);

        // initialize the header
        Set<VCFHeaderLine> headerInfo = getHeaderInfo(UAC, annotationEngine, dbsnp);
        headerInfo.addAll(genotypingEngine.getAppropriateVCFInfoHeaders());

        // invoke initialize() method on each of the annotation classes, allowing them to add their own header lines
        // and perform any necessary initialization/validation steps
        annotationEngine.invokeAnnotationInitializationMethods(headerInfo);

        final Set<String> samplesForHeader;
        if ( ! onlyEmitSamples.isEmpty() ) {
            // make sure that onlyEmitSamples is a subset of samples
            if ( ! sampleNameSet.containsAll(onlyEmitSamples) )
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