The C++ Cuttlefish 3

There is a C++ implementation of Cuttlefish 3 alongside the Rust one. It was the initial version of Cuttlefish 3 — the first careful implementation of the new algorithm — and the Rust implementation that was developed alongside it is now the canonical, forward-looking one.

Where it is

The cuttlefish3-cpp branch:

git clone https://github.com/COMBINE-lab/cuttlefish.git
cd cuttlefish
git checkout cuttlefish3-cpp

It is built the same way as Cuttlefish 1 and 2, with CMake.

Why it is a separate branch

Developing the two side by side means their outputs can be compared directly, which is how each keeps the other honest — a disagreement between them is a bug in one of them, and that is a far sharper signal than either implementation produces alone. A number of correctness fixes were made to the C++ Cuttlefish 3 over this period, and the cuttlefish3-cpp branch carries them.

The two live on separate branches simply because they are separate codebases with separate build systems. The main branch, where the Rust Cuttlefish 3 is developed, has the C++ sources removed entirely so that a checkout of either branch is one implementation and one build.

Which should you use?

• For Cuttlefish 3 — colored graphs, positional colors, collection-scale external-memory construction — use the Rust implementation. It is the released, canonical Cuttlefish 3, and where all new work lands.
• The C++ Cuttlefish 3 is the right thing to reach for if you are reproducing or extending the cross-implementation comparisons, or if you need to check a result the Rust implementation produced against an independent one.
• For Cuttlefish 1 or 2 output formats — GFA, sequence tilings — see Cuttlefish 1 and 2.