80658fd99e31c1561fdf04ff1f18b8bc25babe85,java/src/org/broadinstitute/sting/analyzecovariates/AnalyzeCovariates.java,AnalyzeCovariatesCLP,writeDataTables,#,186
Before Change
// Loop through the covariate table looking for keys with matching read groups
// BUGBUG: hopefully rewrite this to be more efficient
for( List<? extends Comparable> covariateKey : dataManager.getCollapsedTable(iii).keySet() ) {
if( covariateKey.get(0).toString().equals(readGroup) ) {
output.print( covariateKey.get(1).toString() + "\t" ); // Covariate
RecalDatum thisDatum = dataManager.getCollapsedTable(iii).get(covariateKey);
output.print( String.format("%.3f", thisDatum.getEstimatedQReported()) + "\t" ); // Qreported
output.print( String.format("%.3f", thisDatum.empiricalQualDouble(0)) + "\t" ); // Qempirical
After Change
// Output the header
output.println("Covariate\tQreported\tQempirical\tnMismatches\tnBases");
for( Object covariateKey : ((Map)dataManager.getCollapsedTable(iii).data.get(readGroupKey)).keySet()) {
output.print( covariateKey.toString() + "\t" ); // Covariate
RecalDatum thisDatum = (RecalDatum)((Map)dataManager.getCollapsedTable(iii).data.get(readGroupKey)).get(covariateKey);
output.print( String.format("%.3f", thisDatum.getEstimatedQReported()) + "\t" ); // Qreported