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

Examples of org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.VariantStratifier

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     */
    @Test(dataProvider = "StratifiedEvalTestProvider", dependsOnMethods = {"testBasicOperation"})
    public void testIdentityCombine(StratifiedEvalTestProvider cfg) {
        for ( int i = 0; i < cfg.stratificationObjects.size(); i++ ) {
            initialize(cfg);
            final VariantStratifier toReplace = cfg.stratificationObjects.get(i);
            final VariantStratifier newStrat = cfg.stratificationObjects.get(i);
            final Map<Object, Object> remappedStates = Utils.makeIdentityFunctionMap(newStrat.getAllStates());
            StratificationManager<VariantStratifier, EvaluationContext> combined =
                    VEwalker.stratManager.combineStrats(toReplace, newStrat, EvaluationContext.COMBINER, remappedStates);
            checkStratificationCountsAreExpected(combined, cfg.expectedCounts);
        }
    }
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            if (classMap.containsKey(module)) {
                Class<? extends VariantStratifier> c = classMap.get(module);

                try {
                    VariantStratifier vs = c.newInstance();
                    vs.setVariantEvalWalker(variantEvalWalker);
                    vs.initialize();

                    strats.add(vs);
                } catch (InstantiationException e) {
                    throw new GATKException("Unable to instantiate stratification module '" + c.getSimpleName() + "'");
                } catch (IllegalAccessException e) {
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    private static void setStratificationColumns(final GATKReportTable table,
                                                 final String primaryKey,
                                                 final List<Pair<VariantStratifier, Object>> stratsAndStates) {
        table.set(primaryKey, table.getTableName(), table.getTableName());
        for ( final Pair<VariantStratifier, Object> stratAndState : stratsAndStates ) {
            final VariantStratifier vs = stratAndState.getFirst();
            final String columnName = vs.getName();
            final Object strat = stratAndState.getSecond();
            if ( columnName == null || strat == null )
                throw new ReviewedGATKException("Unexpected null variant stratifier state at " + table + " key = " + primaryKey);
            table.set(primaryKey, columnName, strat);
        }
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Related Classes of org.broadinstitute.gatk.tools.walkers.varianteval.stratifications.VariantStratifier

  • org.broadinstitute.gatk.tools.walkers.varianteval.util.VariantEvalUtils
  • org.broadinstitute.gatk.tools.walkers.varianteval.VariantEvalReportWriter
  • org.broadinstitute.gatk.tools.walkers.varianteval.VariantEvalWalkerUnitTest
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