Program: 90849
Project: 90849
Buggy source:
public V getVertexAt(final int x,final int y,final double tolerance,final V ref){
  final AffineTransform3D transform=getRenderTransformCopy();
  final int currentTimepoint=renderTimepoint;
  final double[] lPos=new double[]{x,y,0};
  final double[] gPos=new double[3];
  final ScreenVertexMath svm=new ScreenVertexMath();
  transform.applyInverse(gPos,lPos);
  boolean found=false;
  index.readLock().lock();
  if (drawEllipsoidSliceProjection) {
    final ConvexPolytope cropPolytopeGlobal=getSurroundingPolytopeGlobal(x,y,transform,currentTimepoint);
    final ClipConvexPolytope<V> ccp=index.getSpatialIndex(currentTimepoint).getClipConvexPolytope();
    ccp.clip(cropPolytopeGlobal);
    final double[] xy=new double[]{x,y};
    final double[] vPos=new double[3];
    double minDist=Double.MAX_VALUE;
    for (    final V v : ccp.getInsideValues()) {
      svm.init(v,transform);
      if (svm.projectionContainsView(xy)) {
        found=true;
        v.localize(vPos);
        final double d=LinAlgHelpers.squareDistance(vPos,gPos);
        if (d < minDist) {
          minDist=d;
          ref.refTo(v);
        }
      }
    }
  }
  if (!found) {
    final NearestNeighborSearch<V> nns=index.getSpatialIndex(currentTimepoint).getNearestNeighborSearch();
    nns.search(RealPoint.wrap(gPos));
    final V v=nns.getSampler().get();
    if (v != null) {
      svm.init(v,transform);
      if (drawEllipsoidSliceIntersection) {
        if (svm.containsGlobal(gPos)) {
          found=true;
          ref.refTo(v);
        }
      }
      if (!found && drawPoints) {
        final double[] p=svm.getViewPos();
        final double dx=p[0] - x;
        final double dy=p[1] - y;
        final double dr=pointRadius + tolerance;
        if (dx * dx + dy * dy <= dr * dr) {
          found=true;
          ref.refTo(v);
        }
      }
    }
  }
  index.readLock().unlock();
  return found ? ref : null;
}

Fixed version (ground truth):
public V getVertexAt(final int x,final int y,final double tolerance,final V ref){
  final AffineTransform3D transform=getRenderTransformCopy();
  final int currentTimepoint=renderTimepoint;
  final double[] lPos=new double[]{x,y,0};
  final double[] gPos=new double[3];
  final ScreenVertexMath svm=new ScreenVertexMath();
  transform.applyInverse(gPos,lPos);
  boolean found=false;
  index.readLock().lock();
  if (drawEllipsoidSliceProjection) {
    final ConvexPolytope cropPolytopeGlobal=getSurroundingPolytopeGlobal(x,y,transform,currentTimepoint);
    final ClipConvexPolytope<V> ccp=index.getSpatialIndex(currentTimepoint).getClipConvexPolytope();
    ccp.clip(cropPolytopeGlobal);
    final double[] xy=new double[]{x,y};
    final double[] vPos=new double[3];
    double minDist=Double.MAX_VALUE;
    for (    final V v : ccp.getInsideValues()) {
      svm.init(v,transform);
      if (svm.projectionContainsView(xy)) {
        found=true;
        v.localize(vPos);
        final double d=LinAlgHelpers.squareDistance(vPos,gPos);
        if (d < minDist) {
          minDist=d;
          ref.refTo(v);
        }
      }
    }
  }
  if (!found && drawEllipsoidSliceIntersection) {
    final IncrementalNearestNeighborSearch<V> inns=index.getSpatialIndex(currentTimepoint).getIncrementalNearestNeighborSearch();
    final double maxSquDist=graph.getMaxBoundingSphereRadiusSquared(currentTimepoint);
    inns.search(RealPoint.wrap(gPos));
    while (inns.hasNext()) {
      final V v=inns.next();
      if (inns.getSquareDistance() > maxSquDist)       break;
      svm.init(v,transform);
      if (svm.containsGlobal(gPos)) {
        found=true;
        ref.refTo(v);
        break;
      }
    }
  }
  if (!found && drawPoints) {
    final NearestNeighborSearch<V> nns=index.getSpatialIndex(currentTimepoint).getNearestNeighborSearch();
    nns.search(RealPoint.wrap(gPos));
    final V v=nns.getSampler().get();
    if (v != null) {
      svm.init(v,transform);
      final double[] p=svm.getViewPos();
      final double dx=p[0] - x;
      final double dy=p[1] - y;
      final double dr=pointRadius + tolerance;
      if (dx * dx + dy * dy <= dr * dr) {
        found=true;
        ref.refTo(v);
      }
    }
  }
  index.readLock().unlock();
  return found ? ref : null;
}