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