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);