Package edu.cornell.med.icb.goby.counts

Examples of edu.cornell.med.icb.goby.counts.CountBinningAdaptor.nextTransition()


            int position = binAdaptor.getPosition();
            ObjectArrayList<LocusScore> result = new ObjectArrayList<LocusScore>();
            result.add(new BasicScore(initialStartPosition, position, 0.0f));
            while (binAdaptor.hasNextTransition() && position < endLocation) {
                binAdaptor.nextTransition();
                // position is the zero-based position before the count is changed by the transition
                position = binAdaptor.getPosition();
                // count is how many reads cover the length bases that follow position.
                final double count = selectedWindowFunction == WindowFunction.mean ? binAdaptor.getAverage() : binAdaptor.getMax();
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