writeCSV(files.getFirst(), original, "ORIGINAL", requestedCovariates, false);
outputRecalibrationPlot(files, keepIntermediates);
}
private static void writeCSV(final PrintStream deltaTableFile, final RecalibrationTables recalibrationTables, final String recalibrationMode, final Covariate[] requestedCovariates, final boolean printHeader) {
final NestedHashMap deltaTable = new NestedHashMap();
<BUG>final IntegerIndexedNestedHashMap<RecalDatum> qualTable = recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE);

for (final IntegerIndexedNestedHashMap.Leaf leaf : qualTable.getAllLeaves()) {                                  // go through every element in the covariates table to create the delta table
</BUG>
final int[] newCovs = new int[4];

writeCSV(files.getFirst(), original, "ORIGINAL", requestedCovariates, false);
outputRecalibrationPlot(files, keepIntermediates);
}
private static void writeCSV(final PrintStream deltaTableFile, final RecalibrationTables recalibrationTables, final String recalibrationMode, final Covariate[] requestedCovariates, final boolean printHeader) {
final NestedHashMap deltaTable = new NestedHashMap();
final NestedIntegerArray<RecalDatum> qualTable = recalibrationTables.getTable(RecalibrationTables.TableType.QUALITY_SCORE_TABLE);
for (final NestedIntegerArray.Leaf leaf : qualTable.getAllLeaves()) {                                           // go through every element in the covariates table to create the delta table
final int[] newCovs = new int[4];
