Program: 30646
Project: 30646
Buggy source:
public int instanceMain(final String[] argv){
  if (!parseArgs(argv)) {
    return 1;
  }
  System.setProperty("String_Node_Str","String_Node_Str");
  final Date startDate=new Date();
  this.defaultHeaders.add(new StringHeader(commandLine));
  this.defaultHeaders.add(new StringHeader("String_Node_Str" + startDate));
  Log.setGlobalLogLevel(VERBOSITY);
  SAMFileReader.ValidationStringency originalStringency=SAMFileReader.getDefaultValidationStringency();
  SAMFileReader.setDefaultValidationStringency(VALIDATION_STRINGENCY);
  BlockCompressedOutputStream.setDefaultCompressionLevel(COMPRESSION_LEVEL);
  if (MAX_RECORDS_IN_RAM != null) {
    SAMFileWriterImpl.setDefaultMaxRecordsInRam(MAX_RECORDS_IN_RAM);
  }
  if (CREATE_INDEX) {
    SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(true);
  }
  SAMFileWriterFactory.setDefaultCreateMd5File(CREATE_MD5_FILE);
  if (!TMP_DIR.exists()) {
    TMP_DIR.mkdirs();
  }
  System.setProperty("String_Node_Str",TMP_DIR.getAbsolutePath());
  if (!QUIET) {
    System.err.println("String_Node_Str" + new Date() + "String_Node_Str"+ commandLine);
  }
  final int ret;
  try {
    ret=doWork();
  }
  finally {
    SAMFileReader.setDefaultValidationStringency(originalStringency);
    try {
      if (!QUIET) {
        final Date endDate=new Date();
        final double elapsedMinutes=(endDate.getTime() - startDate.getTime()) / (1000d * 60d);
        final String elapsedString=new DecimalFormat("String_Node_Str").format(elapsedMinutes);
        System.err.println("String_Node_Str" + endDate + "String_Node_Str"+ getClass().getName()+ "String_Node_Str"+ elapsedString+ "String_Node_Str");
        System.err.println("String_Node_Str" + Runtime.getRuntime().totalMemory());
      }
    }
 catch (    Throwable e) {
    }
  }
  return ret;
}

Fixed version (ground truth):
public int instanceMain(final String[] argv){
  if (!parseArgs(argv)) {
    return 1;
  }
  final Date startDate=new Date();
  this.defaultHeaders.add(new StringHeader(commandLine));
  this.defaultHeaders.add(new StringHeader("String_Node_Str" + startDate));
  Log.setGlobalLogLevel(VERBOSITY);
  SAMFileReader.ValidationStringency originalStringency=SAMFileReader.getDefaultValidationStringency();
  SAMFileReader.setDefaultValidationStringency(VALIDATION_STRINGENCY);
  BlockCompressedOutputStream.setDefaultCompressionLevel(COMPRESSION_LEVEL);
  if (MAX_RECORDS_IN_RAM != null) {
    SAMFileWriterImpl.setDefaultMaxRecordsInRam(MAX_RECORDS_IN_RAM);
  }
  if (CREATE_INDEX) {
    SAMFileWriterFactory.setDefaultCreateIndexWhileWriting(true);
  }
  SAMFileWriterFactory.setDefaultCreateMd5File(CREATE_MD5_FILE);
  if (!TMP_DIR.exists()) {
    TMP_DIR.mkdirs();
  }
  System.setProperty("String_Node_Str",TMP_DIR.getAbsolutePath());
  if (!QUIET) {
    System.err.println("String_Node_Str" + new Date() + "String_Node_Str"+ commandLine);
  }
  final int ret;
  try {
    ret=doWork();
  }
  finally {
    SAMFileReader.setDefaultValidationStringency(originalStringency);
    try {
      if (!QUIET) {
        final Date endDate=new Date();
        final double elapsedMinutes=(endDate.getTime() - startDate.getTime()) / (1000d * 60d);
        final String elapsedString=new DecimalFormat("String_Node_Str").format(elapsedMinutes);
        System.err.println("String_Node_Str" + endDate + "String_Node_Str"+ getClass().getName()+ "String_Node_Str"+ elapsedString+ "String_Node_Str");
        System.err.println("String_Node_Str" + Runtime.getRuntime().totalMemory());
      }
    }
 catch (    Throwable e) {
    }
  }
  return ret;
}