Package org.broadinstitute.gatk.engine.walkers

Examples of org.broadinstitute.gatk.engine.walkers.Window.stop()

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        // Retrieve information about the window being accessed.
        if( walker.getClass().isAnnotationPresent(Reference.class) ) {
            Window window = walker.getClass().getAnnotation(Reference.class).window();

            if( window.start() > 0 ) throw new ReviewedGATKException( "Reference window starts after current locus" );
            if( window.stop() < 0 ) throw new ReviewedGATKException( "Reference window ends before current locus" );

            windowStart = window.start();
            windowStop = window.stop();
        }
        else {
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            if( window.start() > 0 ) throw new ReviewedGATKException( "Reference window starts after current locus" );
            if( window.stop() < 0 ) throw new ReviewedGATKException( "Reference window ends before current locus" );

            windowStart = window.start();
            windowStop = window.stop();
        }
        else {
            windowStart = 0;
            windowStop = 0;
        }
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