Program: 13773
Project: 13773
Buggy source:
public int GetOptions(String[] args,Configuration halvadeConf) throws IOException, URISyntaxException {
  try {
    parseArguments(args);
    localRef=tmpDir + "String_Node_Str";
    getBestDistribution(halvadeConf);
    MyConf.setTasksPerNode(halvadeConf,reducersPerContainer);
    MyConf.setScratchTempDir(halvadeConf,tmpDir);
    MyConf.setRefOnHDFS(halvadeConf,ref);
    MyConf.setRefOnScratch(halvadeConf,localRef);
    MyConf.setKnownSitesOnHDFS(halvadeConf,hdfsSites);
    MyConf.setNumThreads(halvadeConf,mthreads);
    MyConf.setGATKNumDataThreads(halvadeConf,GATKdataThreads);
    MyConf.setGATKNumCPUThreads(halvadeConf,GATKCPUThreads);
    MyConf.setNumNodes(halvadeConf,mappers);
    MyConf.setIsPaired(halvadeConf,paired);
    if (exomeBedFile != null)     MyConf.setExomeBed(halvadeConf,exomeBedFile);
    MyConf.setFastqEncoding(halvadeConf,FASTQ_ENCODING[0]);
    MyConf.setOutDir(halvadeConf,out);
    MyConf.setKeepFiles(halvadeConf,keepFiles);
    MyConf.setUseBedTools(halvadeConf,useBedTools);
    MyConf.clearTaskFiles(halvadeConf);
    MyConf.setUseIPrep(halvadeConf,useIPrep);
    MyConf.setUseUnifiedGenotyper(halvadeConf,useGenotyper);
    MyConf.setReuseJVM(halvadeConf,reuseJVM);
    MyConf.setReadGroup(halvadeConf,"String_Node_Str" + RGID + "String_Node_Str"+ RGLB+ "String_Node_Str"+ RGPL+ "String_Node_Str"+ RGPU+ "String_Node_Str"+ RGSM);
    MyConf.setkeepChrSplitPairs(halvadeConf,keepChrSplitPairs);
    if (ca_bwa_aln != null)     MyConf.setBwaAlnArgs(halvadeConf,ca_bwa_aln);
    if (ca_bwa_mem != null)     MyConf.setBwaMemArgs(halvadeConf,ca_bwa_mem);
    if (ca_bwa_samxe != null)     MyConf.setBwaSamxeArgs(halvadeConf,ca_bwa_samxe);
    if (ca_elprep != null)     MyConf.setElPrepArgs(halvadeConf,ca_elprep);
    if (ca_samtools_view != null)     MyConf.setSamtoolsViewArgs(halvadeConf,ca_samtools_view);
    if (ca_bedtools_dbsnp != null)     MyConf.setBedToolsDbSnpArgs(halvadeConf,ca_bedtools_dbsnp);
    if (ca_bedtools_exome != null)     MyConf.setBedToolsExomeArgs(halvadeConf,ca_bedtools_exome);
    if (ca_picard_bai != null)     MyConf.setPicardBaiArgs(halvadeConf,ca_picard_bai);
    if (ca_picard_rg != null)     MyConf.setPicardAddReadGroupArgs(halvadeConf,ca_picard_rg);
    if (ca_picard_dedup != null)     MyConf.setPicardMarkDupArgs(halvadeConf,ca_picard_dedup);
    if (ca_picard_clean != null)     MyConf.setPicardCleanSamArgs(halvadeConf,ca_picard_clean);
    if (ca_gatk_rtc != null)     MyConf.setGatkRealignerTargetCreatorArgs(halvadeConf,ca_gatk_rtc);
    if (ca_gatk_ir != null)     MyConf.setGatkIndelRealignerArgs(halvadeConf,ca_gatk_ir);
    if (ca_gatk_br != null)     MyConf.setGatkBaseRecalibratorArgs(halvadeConf,ca_gatk_br);
    if (ca_gatk_pr != null)     MyConf.setGatkPrintReadsArgs(halvadeConf,ca_gatk_pr);
    if (ca_gatk_cv != null)     MyConf.setGatkCombineVariantsArgs(halvadeConf,ca_gatk_cv);
    if (ca_gatk_vc != null)     MyConf.setGatkVariantCallerArgs(halvadeConf,ca_gatk_vc);
    if (chr != null)     MyConf.setChrList(halvadeConf,chr);
    if (java != null)     MyConf.setJava(halvadeConf,java);
    if (stand_call_conf > 0)     MyConf.setSCC(halvadeConf,stand_call_conf);
    if (stand_emit_conf > 0)     MyConf.setSEC(halvadeConf,stand_emit_conf);
    FileSystem fs=FileSystem.get(new URI(out),halvadeConf);
    if (fs.exists(new Path(out)) && !justCombine) {
      Logger.INFO("String_Node_Str" + out + "String_Node_Str");
      Logger.INFO("String_Node_Str");
      fs.delete(new Path(out),true);
    }
    parseANNFile(halvadeConf);
    setKeysPerChromosome();
    MyConf.setMinChrLength(halvadeConf,minChrLength);
    MyConf.setMultiplier(halvadeConf,multiplier);
    getNumberOfRegions(halvadeConf);
    if (!halvadeDir.endsWith("String_Node_Str"))     halvadeDir+="String_Node_Str";
  }
 catch (  ParseException e) {
    System.err.println("String_Node_Str" + 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 halvadeConf) throws IOException, URISyntaxException {
  try {
    parseArguments(args);
    localRefDir=tmpDir;
    getBestDistribution(halvadeConf);
    HalvadeConf.setTasksPerNode(halvadeConf,reducersPerContainer);
    HalvadeConf.setScratchTempDir(halvadeConf,tmpDir);
    HalvadeConf.setRefOnHDFS(halvadeConf,ref);
    HalvadeConf.setStarDirOnHDFS(halvadeConf,STARGenome);
    HalvadeConf.setRefDirOnScratch(halvadeConf,localRefDir);
    HalvadeConf.setKnownSitesOnHDFS(halvadeConf,hdfsSites);
    HalvadeConf.setNumThreads(halvadeConf,mthreads);
    HalvadeConf.setGATKNumDataThreads(halvadeConf,GATKdataThreads);
    HalvadeConf.setGATKNumCPUThreads(halvadeConf,GATKCPUThreads);
    HalvadeConf.setNumNodes(halvadeConf,mappers);
    HalvadeConf.setIsPaired(halvadeConf,paired);
    if (exomeBedFile != null)     HalvadeConf.setExomeBed(halvadeConf,exomeBedFile);
    HalvadeConf.setOutDir(halvadeConf,out);
    HalvadeConf.setKeepFiles(halvadeConf,keepFiles);
    HalvadeConf.setUseBedTools(halvadeConf,useBedTools);
    HalvadeConf.clearTaskFiles(halvadeConf);
    HalvadeConf.setUseIPrep(halvadeConf,useIPrep);
    HalvadeConf.setUseUnifiedGenotyper(halvadeConf,useGenotyper);
    HalvadeConf.setReuseJVM(halvadeConf,reuseJVM);
    HalvadeConf.setReadGroup(halvadeConf,"String_Node_Str" + RGID + "String_Node_Str"+ RGLB+ "String_Node_Str"+ RGPL+ "String_Node_Str"+ RGPU+ "String_Node_Str"+ RGSM);
    HalvadeConf.setkeepChrSplitPairs(halvadeConf,keepChrSplitPairs);
    if (ca_bwa_aln != null)     HalvadeConf.setBwaAlnArgs(halvadeConf,ca_bwa_aln);
    if (ca_bwa_mem != null)     HalvadeConf.setBwaMemArgs(halvadeConf,ca_bwa_mem);
    if (ca_bwa_samxe != null)     HalvadeConf.setBwaSamxeArgs(halvadeConf,ca_bwa_samxe);
    if (ca_elprep != null)     HalvadeConf.setElPrepArgs(halvadeConf,ca_elprep);
    if (ca_samtools_view != null)     HalvadeConf.setSamtoolsViewArgs(halvadeConf,ca_samtools_view);
    if (ca_bedtools_dbsnp != null)     HalvadeConf.setBedToolsDbSnpArgs(halvadeConf,ca_bedtools_dbsnp);
    if (ca_bedtools_exome != null)     HalvadeConf.setBedToolsExomeArgs(halvadeConf,ca_bedtools_exome);
    if (ca_picard_bai != null)     HalvadeConf.setPicardBaiArgs(halvadeConf,ca_picard_bai);
    if (ca_picard_rg != null)     HalvadeConf.setPicardAddReadGroupArgs(halvadeConf,ca_picard_rg);
    if (ca_picard_dedup != null)     HalvadeConf.setPicardMarkDupArgs(halvadeConf,ca_picard_dedup);
    if (ca_picard_clean != null)     HalvadeConf.setPicardCleanSamArgs(halvadeConf,ca_picard_clean);
    if (ca_gatk_rtc != null)     HalvadeConf.setGatkRealignerTargetCreatorArgs(halvadeConf,ca_gatk_rtc);
    if (ca_gatk_ir != null)     HalvadeConf.setGatkIndelRealignerArgs(halvadeConf,ca_gatk_ir);
    if (ca_gatk_br != null)     HalvadeConf.setGatkBaseRecalibratorArgs(halvadeConf,ca_gatk_br);
    if (ca_gatk_pr != null)     HalvadeConf.setGatkPrintReadsArgs(halvadeConf,ca_gatk_pr);
    if (ca_gatk_cv != null)     HalvadeConf.setGatkCombineVariantsArgs(halvadeConf,ca_gatk_cv);
    if (ca_gatk_vc != null)     HalvadeConf.setGatkVariantCallerArgs(halvadeConf,ca_gatk_vc);
    if (chr != null)     HalvadeConf.setChrList(halvadeConf,chr);
    if (java != null)     HalvadeConf.setJava(halvadeConf,java);
    if (stand_call_conf > 0)     HalvadeConf.setSCC(halvadeConf,stand_call_conf);
    if (stand_emit_conf > 0)     HalvadeConf.setSEC(halvadeConf,stand_emit_conf);
    FileSystem fs=FileSystem.get(new URI(out),halvadeConf);
    if (fs.exists(new Path(out)) && !justCombine) {
      Logger.INFO("String_Node_Str" + out + "String_Node_Str");
      Logger.INFO("String_Node_Str");
      fs.delete(new Path(out),true);
    }
    parseDictFile(halvadeConf);
    ChromosomeSplitter splitter=new ChromosomeSplitter(dict,chr,reducers);
    HalvadeConf.setMinChrLength(halvadeConf,splitter.getRegionSize());
    reducers=splitter.getRegionCount();
    HalvadeConf.setReducers(halvadeConf,reducers);
  }
 catch (  ParseException e) {
    System.err.println("String_Node_Str" + e.getMessage());
    HelpFormatter formatter=new HelpFormatter();
    formatter.setWidth(80);
    formatter.printHelp("String_Node_Str" + "String_Node_Str",options);
    return 1;
  }
  return 0;
}