Program: 13708
Project: 13708
Buggy source:
public int GetOptions(String[] args,Configuration hConf) throws IOException, URISyntaxException {
  try {
    boolean result=parseArguments(args,hConf);
    if (!result) {
      HelpFormatter formatter=new HelpFormatter();
      formatter.setWidth(80);
      formatter.printHelp("String_Node_Str" + "String_Node_Str",options);
      return 1;
    }
    onedec=new DecimalFormat("String_Node_Str");
    if (localRefDir == null) {
      localRefDir=tmpDir;
    }
    HalvadeConf.setScratchTempDir(hConf,tmpDir);
    HalvadeConf.setRefDirOnScratch(hConf,localRefDir);
    HalvadeConf.setRefOnHDFS(hConf,ref);
    if (STARGenome != null) {
      HalvadeConf.setStarDirOnHDFS(hConf,STARGenome);
    }
    HalvadeConf.setKnownSitesOnHDFS(hConf,hdfsSites);
    HalvadeConf.setIsPaired(hConf,paired);
    HalvadeConf.setIsRNA(hConf,rnaPipeline);
    if (bedFile != null) {
      HalvadeConf.setBed(hConf,bedFile);
    }
    if (filterBed != null) {
      HalvadeConf.setFilterBed(hConf,filterBed);
    }
    HalvadeConf.setInputIsBam(hConf,useBamInput);
    HalvadeConf.setOutDir(hConf,out);
    HalvadeConf.setKeepFiles(hConf,keepFiles);
    HalvadeConf.setFilterDBSnp(hConf,filterDBSnp);
    HalvadeConf.clearTaskFiles(hConf);
    HalvadeConf.setUseElPrep(hConf,useElPrep);
    HalvadeConf.setUseUnifiedGenotyper(hConf,useGenotyper);
    HalvadeConf.setRedistribute(hConf,redistribute);
    HalvadeConf.setReadGroup(hConf,"String_Node_Str" + RGID + "String_Node_Str"+ RGLB+ "String_Node_Str"+ RGPL+ "String_Node_Str"+ RGPU+ "String_Node_Str"+ RGSM);
    HalvadeConf.setkeepChrSplitPairs(hConf,keepChrSplitPairs);
    if (STARGenome != null) {
      HalvadeConf.setStarDirPass2HDFS(hConf,out);
    }
    if (chr != null) {
      HalvadeConf.setChrList(hConf,chr);
    }
    if (java != null) {
      HalvadeConf.setJava(hConf,java);
    }
    if (gff != null) {
      HalvadeConf.setGff(hConf,gff);
    }
    if (stand_call_conf > 0) {
      HalvadeConf.setSCC(hConf,stand_call_conf);
    }
    if (stand_emit_conf > 0) {
      HalvadeConf.setSEC(hConf,stand_emit_conf);
    }
    parseDictFile(hConf);
    double inputSize=getInputSize(in,hConf);
    if (coverage == -1.0) {
      coverage=Math.max(1.0,DEFAULT_COVERAGE * (inputSize / DEFAULT_COVERAGE_SIZE));
    }
    Logger.DEBUG("String_Node_Str" + roundOneDecimal(coverage));
    reduces=(int)(coverage * REDUCE_TASKS_FACTOR);
    Logger.DEBUG("String_Node_Str" + reduces);
    ChromosomeSplitter splitter;
    if (bedFile != null)     splitter=new ChromosomeSplitter(dict,bedFile,reduces);
 else     splitter=new ChromosomeSplitter(dict,reduces);
    String bedRegions=out + "String_Node_Str";
    splitter.exportSplitter(bedRegions,hConf);
    reduces=splitter.getRegionCount();
    Logger.DEBUG("String_Node_Str" + reduces);
    HalvadeConf.setBedRegions(hConf,bedRegions);
  }
 catch (  ParseException e) {
    Logger.DEBUG(e.getMessage());
    HelpFormatter formatter=new HelpFormatter();
    formatter.setWidth(80);
    formatter.printHelp("String_Node_Str" + "String_Node_Str",options);
    return 1;
  }
  return 0;
}

Fixed version (ground truth):
public int GetOptions(String[] args,Configuration hConf) throws IOException, URISyntaxException {
  try {
    boolean result=parseArguments(args,hConf);
    if (!result) {
      HelpFormatter formatter=new HelpFormatter();
      formatter.setWidth(80);
      formatter.printHelp("String_Node_Str" + "String_Node_Str",options);
      return 1;
    }
    onedec=new DecimalFormat("String_Node_Str");
    if (localRefDir == null) {
      localRefDir=tmpDir;
    }
    HalvadeConf.setScratchTempDir(hConf,tmpDir);
    HalvadeConf.setRefDirOnScratch(hConf,localRefDir);
    HalvadeConf.setRefOnHDFS(hConf,ref);
    if (STARGenome != null) {
      HalvadeConf.setStarDirOnHDFS(hConf,STARGenome);
    }
    HalvadeConf.setKnownSitesOnHDFS(hConf,hdfsSites);
    HalvadeConf.setIsPaired(hConf,paired);
    HalvadeConf.setIsRNA(hConf,rnaPipeline);
    if (bedFile != null) {
      HalvadeConf.setBed(hConf,bedFile);
    }
    if (filterBed != null) {
      HalvadeConf.setFilterBed(hConf,filterBed);
    }
    HalvadeConf.setInputIsBam(hConf,useBamInput);
    HalvadeConf.setOutDir(hConf,out);
    HalvadeConf.setKeepFiles(hConf,keepFiles);
    HalvadeConf.setFilterDBSnp(hConf,filterDBSnp);
    HalvadeConf.clearTaskFiles(hConf);
    HalvadeConf.setUseElPrep(hConf,useElPrep);
    HalvadeConf.setUseUnifiedGenotyper(hConf,useGenotyper);
    HalvadeConf.setRedistribute(hConf,redistribute);
    HalvadeConf.setReadGroup(hConf,"String_Node_Str" + RGID + "String_Node_Str"+ RGLB+ "String_Node_Str"+ RGPL+ "String_Node_Str"+ RGPU+ "String_Node_Str"+ RGSM);
    HalvadeConf.setkeepChrSplitPairs(hConf,keepChrSplitPairs);
    if (STARGenome != null) {
      HalvadeConf.setStarDirPass2HDFS(hConf,out);
    }
    if (chr != null) {
      HalvadeConf.setChrList(hConf,chr);
    }
    if (java != null) {
      HalvadeConf.setJava(hConf,java);
    }
    if (gff != null) {
      HalvadeConf.setGff(hConf,gff);
    }
    if (stand_call_conf > 0) {
      HalvadeConf.setSCC(hConf,stand_call_conf);
    }
    if (stand_emit_conf > 0) {
      HalvadeConf.setSEC(hConf,stand_emit_conf);
    }
    parseDictFile(hConf);
    double inputSize=getInputSize(in,hConf);
    if (coverage == -1.0) {
      coverage=Math.max(1.0,DEFAULT_COVERAGE * (inputSize / DEFAULT_COVERAGE_SIZE));
    }
    Logger.DEBUG("String_Node_Str" + roundOneDecimal(coverage));
    reduces=(int)(coverage * REDUCE_TASKS_FACTOR);
    Logger.DEBUG("String_Node_Str" + reduces);
    ChromosomeSplitter splitter;
    if (bedFile != null)     splitter=new ChromosomeSplitter(dict,bedFile,reduces);
 else     if (readCountsPerRegionFile != null)     splitter=new ChromosomeSplitter(dict,readCountsPerRegionFile,reduces,reorderRegions);
 else     splitter=new ChromosomeSplitter(dict,reduces);
    String bedRegions=out + "String_Node_Str";
    splitter.exportSplitter(bedRegions,hConf);
    reduces=splitter.getRegionCount();
    Logger.DEBUG("String_Node_Str" + reduces);
    HalvadeConf.setBedRegions(hConf,bedRegions);
  }
 catch (  ParseException e) {
    Logger.DEBUG(e.getMessage());
    HelpFormatter formatter=new HelpFormatter();
    formatter.setWidth(80);
    formatter.printHelp("String_Node_Str" + "String_Node_Str",options);
    return 1;
  }
  return 0;
}