Program: 161288
Project: 161288
Buggy source:
@Override public Collection<Throwable> call() throws Exception {
  final List<String> args=getInputFiles();
  if (getRegion() == null) {
    return wrapException("String_Node_Str");
  }
  if (args.isEmpty()) {
    this.bamFile=null;
  }
 else   if (args.size() == 1) {
    this.bamFile=new File(args.get(0));
  }
 else {
    return wrapException("String_Node_Str");
  }
  if (getWIDTH() < 100) {
    LOG.info("String_Node_Str");
    setWIDTH(100);
  }
  SamReader samFileReader=null;
  try {
    if (getReferenceFile() != null) {
      LOG.info("String_Node_Str");
      this.indexedFastaSequenceFile=new IndexedFastaSequenceFile(getReferenceFile());
    }
    SamReaderFactory srf=SamReaderFactory.makeDefault().validationStringency(ValidationStringency.LENIENT);
    if (this.bamFile == null) {
      LOG.warn("String_Node_Str");
      samFileReader=srf.open(SamInputResource.of(stdin()));
    }
 else {
      LOG.info("String_Node_Str" + this.bamFile);
      samFileReader=srf.open(this.bamFile);
    }
    final SAMFileHeader header=samFileReader.getFileHeader();
    this.interval=IntervalUtils.parseOne(header.getSequenceDictionary(),region);
    if (this.interval == null) {
      return wrapException("String_Node_Str" + region + "String_Node_Str");
    }
    BufferedImage img=build(samFileReader);
    samFileReader.close();
    samFileReader=null;
    if (img == null) {
      return wrapException("String_Node_Str");
    }
    if (getOutputFile() == null) {
      ImageIO.write(img,"String_Node_Str",stdout());
    }
 else {
      LOG.info("String_Node_Str" + getOutputFile());
      ImageIO.write(img,"String_Node_Str",getOutputFile());
    }
    return Collections.emptyList();
  }
 catch (  IOException err) {
    return wrapException(err);
  }
 finally {
    CloserUtil.close(indexedFastaSequenceFile);
    CloserUtil.close(samFileReader);
    indexedFastaSequenceFile=null;
  }
}

Fixed version (ground truth):
@Override public Collection<Throwable> call() throws Exception {
  final List<String> args=getInputFiles();
  if (getRegion() == null) {
    return wrapException("String_Node_Str");
  }
  if (args.isEmpty()) {
    this.bamFile=null;
  }
 else   if (args.size() == 1) {
    this.bamFile=new File(args.get(0));
  }
 else {
    return wrapException("String_Node_Str");
  }
  if (getWIDTH() < 100) {
    LOG.info("String_Node_Str");
    setWIDTH(100);
  }
  SamReader samFileReader=null;
  try {
    if (getReferenceFile() != null) {
      LOG.info("String_Node_Str");
      this.indexedFastaSequenceFile=new IndexedFastaSequenceFile(getReferenceFile());
    }
    SamReaderFactory srf=SamReaderFactory.makeDefault().validationStringency(ValidationStringency.LENIENT);
    if (this.bamFile == null) {
      LOG.warn("String_Node_Str");
      samFileReader=srf.open(SamInputResource.of(stdin()));
    }
 else {
      LOG.info("String_Node_Str" + this.bamFile);
      samFileReader=srf.open(this.bamFile);
    }
    final SAMFileHeader header=samFileReader.getFileHeader();
    this.interval=IntervalUtils.parseOne(header.getSequenceDictionary(),region);
    if (this.interval == null) {
      return wrapException("String_Node_Str" + region + "String_Node_Str");
    }
    LOG.info("String_Node_Str" + this.interval);
    BufferedImage img=build(samFileReader);
    samFileReader.close();
    samFileReader=null;
    if (img == null) {
      return wrapException("String_Node_Str");
    }
    if (getOutputFile() == null) {
      ImageIO.write(img,"String_Node_Str",stdout());
    }
 else {
      LOG.info("String_Node_Str" + getOutputFile());
      ImageIO.write(img,"String_Node_Str",getOutputFile());
    }
    return Collections.emptyList();
  }
 catch (  IOException err) {
    return wrapException(err);
  }
 finally {
    CloserUtil.close(indexedFastaSequenceFile);
    CloserUtil.close(samFileReader);
    indexedFastaSequenceFile=null;
  }
}