From e98cda26c2522bee80292705494dca8dcffa1c5c Mon Sep 17 00:00:00 2001 From: Adam Novak Date: Mon, 28 Oct 2024 11:38:26 -0400 Subject: [PATCH] Commit forgotten comment --- .../bdsg/overlays/packed_reference_path_overlay.hpp | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/bdsg/include/bdsg/overlays/packed_reference_path_overlay.hpp b/bdsg/include/bdsg/overlays/packed_reference_path_overlay.hpp index 49a00148..1f805ae0 100644 --- a/bdsg/include/bdsg/overlays/packed_reference_path_overlay.hpp +++ b/bdsg/include/bdsg/overlays/packed_reference_path_overlay.hpp @@ -18,6 +18,14 @@ using namespace handlegraph; /* * An overlay that adds fast access to paths in addition to allowing path * position queries on them. + * + * TODO: Won't work properly with paths hidden from for_each_path_handle on the + * backing graph, since they won't be indexed but we also won't pass any kind + * of queries through to the backign graph for queries we expect to be able to + * fulfil from the index. Unkike in PackedPositionOverlay, we now expect the + * index to have some path data in it, not just offset tables that we wouldn't + * expect to use for hidden (i,e, haplotype) paths. We should make the overlay + * transparent so hidden paths work properly, or remove hidden paths. */ class PackedReferencePathOverlay : public PackedPositionOverlay {