Examples of ApplicationTime()

Examples of org.broadinstitute.gatk.engine.iterators.ReadTransformersMode.ApplicationTime()

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    public void initializeReadTransformers(final Walker walker) {
        // keep a list of the active read transformers sorted based on priority ordering
        List<ReadTransformer> activeTransformers = new ArrayList<ReadTransformer>();

        final ReadTransformersMode overrideMode = WalkerManager.getWalkerAnnotation(walker, ReadTransformersMode.class);
        final ReadTransformer.ApplicationTime overrideTime = overrideMode != null ? overrideMode.ApplicationTime() : null;

        final PluginManager<ReadTransformer> pluginManager = new PluginManager<ReadTransformer>(ReadTransformer.class);

        for ( final ReadTransformer transformer : pluginManager.createAllTypes() ) {
            transformer.initialize(overrideTime, this, walker);
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Examples of org.broadinstitute.gatk.engine.walkers.BAQMode.ApplicationTime()

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        baqHMM = new BAQ(engine.getArguments().BAQGOP);

        if ( qmode == BAQ.QualityMode.DONT_MODIFY )
            throw new ReviewedGATKException("BUG: shouldn't create BAQ transformer with quality mode DONT_MODIFY");

        if ( mode.ApplicationTime() == ReadTransformer.ApplicationTime.FORBIDDEN && enabled() )
            throw new UserException.BadArgumentValue("baq", "Walker cannot accept BAQ'd base qualities, and yet BAQ mode " + cmode + " was requested.");

        return mode.ApplicationTime();
    }
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Examples of org.broadinstitute.gatk.engine.walkers.BAQMode.ApplicationTime()

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            throw new ReviewedGATKException("BUG: shouldn't create BAQ transformer with quality mode DONT_MODIFY");

        if ( mode.ApplicationTime() == ReadTransformer.ApplicationTime.FORBIDDEN && enabled() )
            throw new UserException.BadArgumentValue("baq", "Walker cannot accept BAQ'd base qualities, and yet BAQ mode " + cmode + " was requested.");

        return mode.ApplicationTime();
    }

    @Override
    public boolean enabled() {
        return cmode != BAQ.CalculationMode.OFF;
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