Program: 16606
Project: 16606
Buggy source:
@Override public List<Result> createObjects(double maxEScore) throws IOException, ParseException {
  List<Result> results=new ArrayList();
  log.info("String_Node_Str");
  LineNumberReader lnr=new LineNumberReader(new FileReader(targetFile));
  lnr.skip(Long.MAX_VALUE);
  fileLinesCount=lnr.getLineNumber();
  log.info(fileLinesCount + "String_Node_Str");
  lnr.close();
  FileInputStream fileInputStream=new FileInputStream(targetFile);
  Scanner scanner=new Scanner(fileInputStream);
  String line=fetchData(scanner);
  int lineNumber=1;
  while (scanner.hasNext()) {
    try {
      BlastResultBuilder resultBuilder=new BlastResultBuilder();
      resultBuilder.setQueryID(queryId).setDbFile(databaseFile).setProgram(programName).setQueryDef(queryName).setReference(blastReference);
      List<Hit> hits=new ArrayList();
      String currentQueryId=queryId;
      while (currentQueryId.equals(queryId) && scanner.hasNext()) {
        BlastHitBuilder hitBuilder=new BlastHitBuilder();
        List<Hsp> hsps=new ArrayList();
        String currentSubjectId=subjectId;
        while (currentSubjectId.equals(subjectId) && scanner.hasNext()) {
          if (new Double(evalue) > maxEScore) {
            line=fetchData(scanner);
            lineNumber++;
            continue;
          }
          BlastHspBuilder hspBuilder=new BlastHspBuilder();
          hspBuilder.setHspAlignLen(new Integer(alnLength)).setHspGaps(new Integer(gapOpenCount)).setHspQueryFrom(new Integer(queryStart)).setHspQueryTo(new Integer(queryEnd)).setHspHitFrom(new Integer(subjectStart)).setHspHitTo(new Integer(subjectEnd)).setHspEvalue(new Double(evalue)).setHspBitScore(new Double(bitScore)).setPercentageIdentity(new Double(percIdentity) / 100).setMismatchCount(new Integer(mismatchCount));
          hsps.add(hspBuilder.createBlastHsp());
          line=fetchData(scanner);
          lineNumber++;
        }
        hits.add(hitBuilder.setHsps(hsps).createBlastHit());
      }
      results.add(resultBuilder.setHits(hits).createBlastResult());
    }
 catch (    NumberFormatException e) {
      throw new ParseException("String_Node_Str" + lineNumber + "String_Node_Str"+ line,0);
    }
  }
  return results;
}

Fixed version (ground truth):
@Override public List<Result> createObjects(double maxEScore) throws IOException, ParseException {
  List<Result> results=new ArrayList();
  log.info("String_Node_Str");
  LineNumberReader lnr=new LineNumberReader(new FileReader(targetFile));
  lnr.skip(Long.MAX_VALUE);
  fileLinesCount=lnr.getLineNumber();
  log.info(fileLinesCount + "String_Node_Str");
  lnr.close();
  FileInputStream fileInputStream=new FileInputStream(targetFile);
  Scanner scanner=new Scanner(fileInputStream);
  String line=fetchData(scanner);
  int lineNumber=0;
  while (lineNumber < fileLinesCount) {
    try {
      BlastResultBuilder resultBuilder=new BlastResultBuilder();
      resultBuilder.setQueryID(queryId).setDbFile(databaseFile).setProgram(programName).setQueryDef(queryName).setReference(blastReference);
      List<Hit> hits=new ArrayList();
      String currentQueryId=queryId;
      while (currentQueryId.equals(queryId) && lineNumber < fileLinesCount) {
        BlastHitBuilder hitBuilder=new BlastHitBuilder();
        List<Hsp> hsps=new ArrayList();
        String currentSubjectId=subjectId;
        while (currentSubjectId.equals(subjectId) && lineNumber < fileLinesCount) {
          if (new Double(evalue) > maxEScore) {
            line=fetchData(scanner);
            lineNumber++;
            continue;
          }
          BlastHspBuilder hspBuilder=new BlastHspBuilder();
          hspBuilder.setHspAlignLen(new Integer(alnLength)).setHspGaps(new Integer(gapOpenCount)).setHspQueryFrom(new Integer(queryStart)).setHspQueryTo(new Integer(queryEnd)).setHspHitFrom(new Integer(subjectStart)).setHspHitTo(new Integer(subjectEnd)).setHspEvalue(new Double(evalue)).setHspBitScore(new Double(bitScore)).setPercentageIdentity(new Double(percIdentity) / 100).setMismatchCount(new Integer(mismatchCount));
          hsps.add(hspBuilder.createBlastHsp());
          if (scanner.hasNext())           line=fetchData(scanner);
          lineNumber++;
        }
        hits.add(hitBuilder.setHsps(hsps).createBlastHit());
      }
      results.add(resultBuilder.setHits(hits).createBlastResult());
    }
 catch (    NumberFormatException e) {
      throw new ParseException("String_Node_Str" + lineNumber + "String_Node_Str"+ line,0);
    }
  }
  return results;
}