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

org.broadinstitute.gatk.engine.iterators.ReadTransformer

Baseclass used to describe a read transformer like BAQ and BQSR Read transformers are plugable infrastructure that modify read state either on input, on output, or within walkers themselves. The function apply() is called on each read seen by the GATK (after passing all ReadFilters) and it can do as it sees fit (without modifying the alignment) to the read to change qualities, add tags, etc. Initialize is called once right before the GATK traversal begins providing the ReadTransformer with the ability to collect and initialize data from the engine. Note that all ReadTransformers within the classpath are created and initialized. If one shouldn't be run it should look at the command line options of the engine and override the enabled. @since 8/31/12 @author depristo

     */
    protected void checkActiveReadTransformers(final List<ReadTransformer> readTransformers) {
        if ( readTransformers == null )
            throw new IllegalArgumentException("read transformers cannot be null");


        ReadTransformer sawMustBeFirst = null;
        ReadTransformer sawMustBeLast  = null;


        for ( final ReadTransformer r : readTransformers ) {
            if ( r.getOrderingConstraint() == ReadTransformer.OrderingConstraint.MUST_BE_FIRST ) {
                if ( sawMustBeFirst != null )
                    throw new UserException.IncompatibleReadFiltersException(sawMustBeFirst.toString(), r.toString());
                sawMustBeFirst = r;
            } else if ( r.getOrderingConstraint() == ReadTransformer.OrderingConstraint.MUST_BE_LAST ) {
                if ( sawMustBeLast != null )
                    throw new UserException.IncompatibleReadFiltersException(sawMustBeLast.toString(), r.toString());
                sawMustBeLast = r;
            }
        }
    }

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

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