86c8c08375b5524aab3d3842de55d3715c8d9914,java/src/org/broadinstitute/sting/playground/gatk/walkers/CovariateCounterWalker.java,CovariateCounterWalker,qualityDiffVsCycle,#,237

Before Change


            }

            for ( RecalData datum: flattenData ) {
                if( !datum.readGroup.equals(readGroup.getReadGroupId()) )
                    continue;
                ByCycle.get(datum.pos).inc(datum.N, datum.B);
                ByCycleReportedQ.get(datum.pos).inc(datum.qual, datum.N);
                All.inc(datum.N, datum.B);
                AllReported.inc(datum.qual, datum.N);

After Change


                ByCycleReportedQ.add(new MeanReportedQuality());
            }

            for ( RecalData datum: getRecalData(readGroup.getReadGroupId()) ) {
                ByCycle.get(datum.pos).inc(datum.N, datum.B);
                ByCycleReportedQ.get(datum.pos).inc(datum.qual, datum.N);
                All.inc(datum.N, datum.B);