Program: 37790
Project: 37790
Buggy source:
private Cell parseOutputStructure(Cell origCell,String outFile){
  if (!(new File(outFile)).exists()) {
    if (GAParameters.getParams().getVerbosity() >= 4)     System.out.println("String_Node_Str");
    return null;
  }
  String output=Utility.readStringFromFile(outFile);
  List<Vect> basis=new LinkedList<Vect>();
  List<Site> sites=new LinkedList<Site>();
  String lines[]=output.split("String_Node_Str");
  int numAtoms=Integer.parseInt(lines[3]);
  String xs[]=lines[5].split("String_Node_Str");
  double xlo=Double.parseDouble(xs[0]);
  double xhi=Double.parseDouble(xs[1]);
  double xy=Double.parseDouble(xs[2]);
  String ys[]=lines[6].split("String_Node_Str");
  double ylo=Double.parseDouble(ys[0]);
  double yhi=Double.parseDouble(ys[1]);
  double xz=Double.parseDouble(ys[2]);
  String zs[]=lines[7].split("String_Node_Str");
  double zlo=Double.parseDouble(zs[0]);
  double zhi=Double.parseDouble(zs[1]);
  double yz=Double.parseDouble(zs[2]);
  basis.add(new Vect(xhi - xlo,0.0,0.0));
  basis.add(new Vect(xy,yhi - ylo,0.0));
  basis.add(new Vect(xz,yz,zhi - zlo));
  for (int i=0; i < numAtoms; i++) {
    String as[]=lines[9 + i].split("String_Node_Str");
    int type=Integer.parseInt(as[1]) - 1;
    double x=Double.parseDouble(as[2]);
    double y=Double.parseDouble(as[3]);
    double z=Double.parseDouble(as[4]);
    sites.add(new Site(origCell.getComposition().getElements().get(type),new Vect(x - xlo,y - ylo,z - zlo)));
  }
  if (origCell.getBasisSize() != numAtoms) {
    System.out.println("String_Node_Str");
    System.out.println(outFile);
  }
  return new Cell(basis,sites,origCell.getLabel());
}

Fixed version (ground truth):
private Cell parseOutputStructure(Cell origCell,String outFile){
  if (!(new File(outFile)).exists()) {
    if (GAParameters.getParams().getVerbosity() >= 4)     System.out.println("String_Node_Str");
    return null;
  }
  String output=Utility.readStringFromFile(outFile);
  List<Vect> basis=new LinkedList<Vect>();
  List<Site> sites=new LinkedList<Site>();
  String lines[]=output.split("String_Node_Str");
  int numAtoms=Integer.parseInt(lines[3]);
  String xs[]=lines[5].split("String_Node_Str");
  double xlo_bound=Double.parseDouble(xs[0]);
  double xhi_bound=Double.parseDouble(xs[1]);
  double xy=Double.parseDouble(xs[2]);
  String ys[]=lines[6].split("String_Node_Str");
  double ylo_bound=Double.parseDouble(ys[0]);
  double yhi_bound=Double.parseDouble(ys[1]);
  double xz=Double.parseDouble(ys[2]);
  String zs[]=lines[7].split("String_Node_Str");
  double zlo_bound=Double.parseDouble(zs[0]);
  double zhi_bound=Double.parseDouble(zs[1]);
  double yz=Double.parseDouble(zs[2]);
  double xlo=xlo_bound - Math.min(Math.min(0.0,xy),Math.min(xz,xy + xz));
  double xhi=xhi_bound - Math.max(Math.max(0.0,xy),Math.max(xz,xy + xz));
  double ylo=ylo_bound - Math.min(0.0,yz);
  double yhi=yhi_bound - Math.max(0.0,yz);
  double zlo=zlo_bound;
  double zhi=zhi_bound;
  basis.add(new Vect(xhi - xlo,0.0,0.0));
  basis.add(new Vect(xy,yhi - ylo,0.0));
  basis.add(new Vect(xz,yz,zhi - zlo));
  for (int i=0; i < numAtoms; i++) {
    String as[]=lines[9 + i].split("String_Node_Str");
    int type=Integer.parseInt(as[1]) - 1;
    double x=Double.parseDouble(as[2]);
    double y=Double.parseDouble(as[3]);
    double z=Double.parseDouble(as[4]);
    sites.add(new Site(origCell.getComposition().getElements().get(type),new Vect(x - xlo,y - ylo,z - zlo)));
  }
  if (origCell.getBasisSize() != numAtoms) {
    System.out.println("String_Node_Str");
    System.out.println(outFile);
  }
  return new Cell(basis,sites,origCell.getLabel());
}