Program: 188995
Project: 188995
Buggy source:
public Set<LaneInfo> parseMiSecData(BufferedReader freader) throws IOException, Exception {
  Set<SampleInfo> samples=new HashSet<SampleInfo>();
  LaneInfo laneInfo=generateLaneInfo("String_Node_Str",4);
  laneInfo.setSamples(samples);
  String[] headerStrings=freader.readLine().split("String_Node_Str");
  List<String> header=Arrays.asList(headerStrings);
  String line;
  while ((line=freader.readLine()) != null) {
    String[] args=line.split("String_Node_Str");
    String[] sampleInfo=args[header.indexOf("String_Node_Str")].split("String_Node_Str");
    String prettyName=args[header.indexOf("String_Node_Str")];
    String projectName=sampleInfo[0];
    String individualNumber=sampleInfo[1];
    String librarySourceTemplateType=null;
    String tissueOrigin=null;
    String tissueType=null;
    String libraryType=null;
    String librarySizeCode=null;
    String targetedResequencing=null;
    String tissuePreparation=null;
    Integer organismId=findOrganismId(args[header.indexOf("String_Node_Str")].split("String_Node_Str")[0].replace('_',' '));
    String barcode=args[header.indexOf("String_Node_Str")];
    if (sampleInfo[2].contains("String_Node_Str")) {
      tissueType="String_Node_Str";
      tissuePreparation="String_Node_Str";
    }
 else     if (sampleInfo[2].contains("String_Node_Str")) {
      tissueType="String_Node_Str";
    }
 else     if (sampleInfo[2].contains("String_Node_Str")) {
      tissueType="String_Node_Str";
    }
 else {
      Log.stdout("String_Node_Str" + prettyName);
    }
    SampleInfo info=generateSampleInfo(prettyName,projectName,individualNumber,librarySourceTemplateType,tissueOrigin,tissueType,libraryType,librarySizeCode,barcode,organismId,targetedResequencing,tissuePreparation);
    String tissueRegion=sampleInfo[2].substring(0,1);
    if (StringUtils.isNumeric(tissueRegion)) {
      info.addSampleAttribute("String_Node_Str",tissueRegion);
    }
    samples.add(info);
  }
  Set<LaneInfo> lanes=new HashSet<LaneInfo>();
  lanes.add(laneInfo);
  return lanes;
}

Fixed version (ground truth):
public Set<LaneInfo> parseMiSecData(BufferedReader freader) throws IOException, Exception {
  Set<SampleInfo> samples=new HashSet<SampleInfo>();
  LaneInfo laneInfo=generateLaneInfo("String_Node_Str",4);
  laneInfo.setSamples(samples);
  String[] headerStrings=freader.readLine().split("String_Node_Str");
  List<String> header=Arrays.asList(headerStrings);
  String line;
  while ((line=freader.readLine()) != null) {
    String[] args=line.split("String_Node_Str");
    String[] sampleInfo=args[header.indexOf("String_Node_Str")].split("String_Node_Str");
    String prettyName=args[header.indexOf("String_Node_Str")];
    String projectName=sampleInfo[0];
    String individualNumber=sampleInfo[1];
    String librarySourceTemplateType=null;
    String tissueOrigin=null;
    String tissueType=null;
    String libraryType=null;
    String librarySizeCode=null;
    String targetedResequencing=null;
    String tissuePreparation=null;
    Integer organismId=findOrganismId(args[header.indexOf("String_Node_Str")].split("String_Node_Str")[0].replace('_',' '));
    String barcode=args[header.indexOf("String_Node_Str")];
    if (sampleInfo[2].contains("String_Node_Str")) {
      tissueType="String_Node_Str";
      tissuePreparation="String_Node_Str";
    }
 else     if (sampleInfo[2].contains("String_Node_Str")) {
      tissueType="String_Node_Str";
    }
 else     if (sampleInfo[2].contains("String_Node_Str")) {
      tissueType="String_Node_Str";
    }
 else {
      Log.stdout("String_Node_Str" + prettyName);
    }
    SampleInfo info=generateSampleInfo(prettyName,projectName,individualNumber,librarySourceTemplateType,tissueOrigin,tissueType,libraryType,librarySizeCode,barcode,organismId,targetedResequencing,tissuePreparation);
    info.setSampleDescription(info.getName());
    info.setIusName(info.getBarcode());
    info.setIusDescription(info.getBarcode());
    String tissueRegion=sampleInfo[2].substring(0,1);
    if (StringUtils.isNumeric(tissueRegion)) {
      info.addSampleAttribute("String_Node_Str",tissueRegion);
    }
    samples.add(info);
  }
  Set<LaneInfo> lanes=new HashSet<LaneInfo>();
  lanes.add(laneInfo);
  return lanes;
}