Package org.broadinstitute.gatk.engine.iterators

Examples of org.broadinstitute.gatk.engine.iterators.ReadTransformersMode


     */
    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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