bubblegun_cpp

bubblegun_cpp is a focused C++ rewrite of BubbleGun's bchains workflow. The current implementation follows the packed-graph path in the Python codebase and keeps the runtime traversal data in dense arrays rather than a dictionary-based graph.

• Supported subcommand: bchains
• Supported options: --bubble_json, --only_simple, --only_super, --save_memory, --chains_gfa
• Not implemented yet: --fasta, --out_haplos, and the other BubbleGun subcommands

• The graph loader stores node metadata once, then builds a two-sided packed adjacency structure from GFA L lines.
• The public graph API is handle-style and exposes oriented node handles through get_handle, flip, and follow_edges.
• Bubble detection uses the same packed superbubble search strategy as the Python implementation, then chains bubbles by shared endpoints and annotates nested superbubbles for JSON compatibility.

The project vendors argparse as a git submodule under external/argparse.

git submodule update --init --recursive
cd /workspace/fawaz/bubblegun_cpp/bubblegun2
cmake -S . -B build
cmake --build build -j

./build/bubblegun_cpp -g /path/to/graph.gfa --log_file run.log bchains

Examples:

./build/bubblegun_cpp -g ../benchmark_graphs/GCA.cleaned.gfa --log_file GCA.cleaned.log bchains
./build/bubblegun_cpp -g ../benchmark_graphs/GCA.cleaned.gfa bchains --bubble_json GCA.cleaned.json
./build/bubblegun_cpp -g ../benchmark_graphs/GCA.cleaned.gfa bchains --only_simple
./build/bubblegun_cpp -g ../benchmark_graphs/GCA.cleaned.gfa bchains --chains_gfa GCA.cleaned.chains.gfa

The requested timing binary for local tests is:

/workspace/fawaz/miniforge/envs/bubblegun_cpp/bin/time -v

Example:

/workspace/fawaz/miniforge/envs/bubblegun_cpp/bin/time -v ./build/bubblegun_cpp -g ../benchmark_graphs/GCA.cleaned.gfa --log_file GCA.cleaned.log bchains