Program: 161278
Project: 161278
Buggy source:
@Override public int doWork(final List<String> args){
  if (this.regionStr == null) {
    LOG.error("String_Node_Str");
    return -1;
  }
  if (this.WIDTH < 100) {
    LOG.info("String_Node_Str");
    this.WIDTH=100;
  }
  SamReader samFileReader=null;
  try {
    final SamReaderFactory srf=super.createSamReaderFactory();
    if (this.referenceFile != null) {
      LOG.info("String_Node_Str");
      this.indexedFastaSequenceFile=new IndexedFastaSequenceFile(this.referenceFile);
      srf.referenceSequence(this.referenceFile);
    }
    final IntervalParser intervalParser=new IntervalParser(this.indexedFastaSequenceFile.getSequenceDictionary()).setFixContigName(true);
    this.interval=intervalParser.parse(this.regionStr);
    if (this.interval == null) {
      LOG.error("String_Node_Str" + regionStr + "String_Node_Str");
      return -1;
    }
    LOG.info("String_Node_Str" + this.interval);
    for (    final String vcfFile : IOUtils.unrollFiles(variants)) {
      final VCFFileReader vcfFileReader=new VCFFileReader(new File(vcfFile),true);
      final CloseableIterator<VariantContext> r=vcfFileReader.query(this.interval.getContig(),this.interval.getStart(),this.interval.getEnd());
      while (r.hasNext()) {
        this.highlightPositions.add(r.next().getStart());
      }
      r.close();
      vcfFileReader.close();
    }
    for (    final String bamFile : IOUtils.unrollFiles(args)) {
      samFileReader=srf.open(SamInputResource.of(bamFile));
      final SAMFileHeader header=samFileReader.getFileHeader();
      final SAMSequenceDictionary dict=header.getSequenceDictionary();
      if (dict == null) {
        LOG.error("String_Node_Str" + bamFile);
        return -1;
      }
      if (dict.getSequence(this.interval.getContig()) == null) {
        LOG.error("String_Node_Str" + bamFile + "String_Node_Str"+ this.interval);
        return -1;
      }
      scan(samFileReader);
      samFileReader.close();
      samFileReader=null;
    }
    if (this.key2partition.isEmpty()) {
      LOG.error("String_Node_Str");
      return -1;
    }
    this.key2partition.values().stream().forEach(P -> P.build());
    int image_width=this.key2partition.values().stream().mapToInt(P -> P.image.getWidth()).max().getAsInt();
    int image_height=this.key2partition.values().stream().mapToInt(P -> P.image.getHeight()).sum();
    final BufferedImage img=new BufferedImage(image_width,image_height,BufferedImage.TYPE_INT_RGB);
    final Graphics2D g=img.createGraphics();
    g.setRenderingHint(RenderingHints.KEY_RENDERING,RenderingHints.VALUE_COLOR_RENDER_QUALITY);
    int y=0;
    for (    final String key : this.key2partition.keySet()) {
      BufferedImage subImg=this.key2partition.get(key).image;
      g.drawImage(subImg,0,y,null);
      y+=subImg.getHeight();
    }
    g.dispose();
    if (this.outputFile == null) {
      ImageIO.write(img,"String_Node_Str",stdout());
    }
 else {
      LOG.info("String_Node_Str" + this.outputFile);
      final String format=(this.outputFile.getName().toLowerCase().endsWith("String_Node_Str") ? "String_Node_Str" : "String_Node_Str");
      ImageIO.write(img,format,this.outputFile);
    }
    return RETURN_OK;
  }
 catch (  Exception err) {
    LOG.error(err);
    return -1;
  }
 finally {
    CloserUtil.close(indexedFastaSequenceFile);
    CloserUtil.close(samFileReader);
    indexedFastaSequenceFile=null;
  }
}

Fixed version (ground truth):
@Override public int doWork(final List<String> args){
  if (this.regionStr == null) {
    LOG.error("String_Node_Str");
    return -1;
  }
  if (this.WIDTH < 100) {
    LOG.info("String_Node_Str");
    this.WIDTH=100;
  }
  SamReader samFileReader=null;
  try {
    final SamReaderFactory srf=super.createSamReaderFactory();
    if (this.referenceFile != null) {
      LOG.info("String_Node_Str");
      this.indexedFastaSequenceFile=new IndexedFastaSequenceFile(this.referenceFile);
      srf.referenceSequence(this.referenceFile);
    }
    final IntervalParser intervalParser=new IntervalParser(this.indexedFastaSequenceFile == null ? null : this.indexedFastaSequenceFile.getSequenceDictionary()).setFixContigName(true);
    this.interval=intervalParser.parse(this.regionStr);
    if (this.interval == null) {
      LOG.error("String_Node_Str" + regionStr + "String_Node_Str");
      return -1;
    }
    LOG.info("String_Node_Str" + this.interval);
    for (    final String vcfFile : IOUtils.unrollFiles(variants)) {
      final VCFFileReader vcfFileReader=new VCFFileReader(new File(vcfFile),true);
      final CloseableIterator<VariantContext> r=vcfFileReader.query(this.interval.getContig(),this.interval.getStart(),this.interval.getEnd());
      while (r.hasNext()) {
        this.highlightPositions.add(r.next().getStart());
      }
      r.close();
      vcfFileReader.close();
    }
    for (    final String bamFile : IOUtils.unrollFiles(args)) {
      samFileReader=srf.open(SamInputResource.of(bamFile));
      final SAMFileHeader header=samFileReader.getFileHeader();
      final SAMSequenceDictionary dict=header.getSequenceDictionary();
      if (dict == null) {
        LOG.error("String_Node_Str" + bamFile);
        return -1;
      }
      if (dict.getSequence(this.interval.getContig()) == null) {
        LOG.error("String_Node_Str" + bamFile + "String_Node_Str"+ this.interval);
        return -1;
      }
      scan(samFileReader);
      samFileReader.close();
      samFileReader=null;
    }
    if (this.key2partition.isEmpty()) {
      LOG.error("String_Node_Str");
      return -1;
    }
    this.key2partition.values().stream().forEach(P -> P.build());
    int image_width=this.key2partition.values().stream().mapToInt(P -> P.image.getWidth()).max().getAsInt();
    int image_height=this.key2partition.values().stream().mapToInt(P -> P.image.getHeight()).sum();
    final BufferedImage img=new BufferedImage(image_width,image_height,BufferedImage.TYPE_INT_RGB);
    final Graphics2D g=img.createGraphics();
    int y=0;
    for (    final String key : this.key2partition.keySet()) {
      BufferedImage subImg=this.key2partition.get(key).image;
      g.drawImage(subImg,0,y,null);
      y+=subImg.getHeight();
    }
    g.dispose();
    if (this.outputFile == null) {
      ImageIO.write(img,"String_Node_Str",stdout());
    }
 else {
      LOG.info("String_Node_Str" + this.outputFile);
      final String format=(this.outputFile.getName().toLowerCase().endsWith("String_Node_Str") ? "String_Node_Str" : "String_Node_Str");
      ImageIO.write(img,format,this.outputFile);
    }
    return RETURN_OK;
  }
 catch (  Exception err) {
    LOG.error(err);
    return -1;
  }
 finally {
    CloserUtil.close(indexedFastaSequenceFile);
    CloserUtil.close(samFileReader);
    indexedFastaSequenceFile=null;
  }
}