Package org.broadinstitute.gatk.tools.walkers.varianteval.util

Examples of org.broadinstitute.gatk.tools.walkers.varianteval.util.EvaluationContext

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    private final void checkStratificationCountsAreExpected(final StratificationManager<VariantStratifier, EvaluationContext> manager,
                                                            final List<Integer> expectedCounts) {
        for ( int key = 0; key < manager.size(); key++ ) {
            final String stratStateString = manager.getStratsAndStatesStringForKey(key);
            final EvaluationContext nec = manager.get(key);

            for ( final VariantEvaluator ve : nec.getVariantEvaluators() ) {
                // test for count here
                final CounterEval counterEval = (CounterEval)ve;
                final int expected = expectedCounts.get(key);
                Assert.assertEquals(counterEval.count, expected, "Count seen of " + counterEval.count + " not expected " + expected + " at " + stratStateString);
            }
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        final GATKReport report = initializeGATKReport(stratifiers, evaluators);

        for ( int key = 0; key < stratManager.size(); key++ ) {
            final String stratStateString = stratManager.getStratsAndStatesStringForKey(key);
            final List<Pair<VariantStratifier, Object>> stratsAndStates = stratManager.getStratsAndStatesForKey(key);
            final EvaluationContext nec = stratManager.get(key);

            for ( final VariantEvaluator ve : nec.getVariantEvaluators() ) {
                final GATKReportTable table = report.getTable(ve.getSimpleName());

                final AnalysisModuleScanner scanner = new AnalysisModuleScanner(ve);
                final Map<Field, DataPoint> datamap = scanner.getData();
                try {
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        final List<VariantStratifier> strats = new ArrayList<VariantStratifier>(stratificationObjects);
        stratManager = new StratificationManager<VariantStratifier, EvaluationContext>(strats);

        logger.info("Creating " + stratManager.size() + " combinatorial stratification states");
        for ( int i = 0; i < stratManager.size(); i++ ) {
            EvaluationContext ec = new EvaluationContext(this, evaluationObjects);
            stratManager.set(i, ec);
        }
    }   
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Related Classes of org.broadinstitute.gatk.tools.walkers.varianteval.util.EvaluationContext

  • org.broadinstitute.gatk.tools.walkers.varianteval.evaluators.VariantEvaluator
  • org.broadinstitute.gatk.tools.walkers.varianteval.VariantEval
  • org.broadinstitute.gatk.tools.walkers.varianteval.VariantEvalReportWriter
  • org.broadinstitute.gatk.tools.walkers.varianteval.VariantEvalWalkerUnitTest
  • org.broadinstitute.gatk.utils.exceptions.ReviewedGATKException
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