if (this.TMP_DIR == null) this.TMP_DIR = new ArrayList<File>();
if (this.TMP_DIR.isEmpty()) TMP_DIR.add(IOUtil.getDefaultTmpDir());
// Build the default headers
final Date startDate = new Date();
this.defaultHeaders.add(new StringHeader(commandLine));
this.defaultHeaders.add(new StringHeader("Started on: " + startDate));
Log.setGlobalLogLevel(VERBOSITY);
final ValidationStringency originalStringency = SAMFileReader.getDefaultValidationStringency();
SAMFileReader.setDefaultValidationStringency(VALIDATION_STRINGENCY);
SamReaderFactory.setDefaultValidationStringency(VALIDATION_STRINGENCY);