if(!intervalFile.equals("")) argList.add("TARGET_REGION="+intervalFile);
final String[] args = new String[argList.size()];
argList.toArray(args);
Assert.assertEquals(new CollectIlluminaSummaryMetrics().instanceMain(args), 0);
final MetricsFile<IlluminaSummaryMetrics, Integer> retVal = new MetricsFile<IlluminaSummaryMetrics, Integer>();
retVal.read(new FileReader(outputFile));
return retVal;
}