Package org.broadinstitute.gatk.engine.walkers

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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            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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