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GFAffix collapses walk-preserving shared affixes
GFAffix identifies walk-preserving shared affixes in variation graphs and collapses them into a non-redundant graph structure.
GFAffix is written in RUST and requires a working RUST build system for installation. See https://www.rust-lang.org/tools/install for more details.
It makes use of the following crates:
- clap
- env_logger
- flate2
- gfa
- handlegraph
- indexmap
- log
- rayon
- regex
- rustc-hash
Make sure you have conda/mamba installed!
mamba install -c conda-forge -c bioconda gfaffix
wget --no-check-certificate -c https://github.com/marschall-lab/GFAffix/releases/download/0.2.2/GFAffix-0.2.2_linux_x86_64.tar.gz
tar -xzvf GFAffix-0.2.2_linux_x86_64.tar.gz
# you are ready to go!
./GFAffix-0.2.2_linux_x86_64/gfaffix
wget --no-check-certificate -c https://github.com/marschall-lab/GFAffix/releases/download/0.2.2/GFAffix-0.2.2_macos_x_arm64.tar.gz
tar -xzvf GFAffix-0.2.2_macos_x_arm64.tar.gz
# you are ready to go!
./GFAffix-0.2.2_macos_x_arm64/gfaffix
# install GFAffix
git clone https://github.com/marschall-lab/GFAffix.git
# build program
cargo build --manifest-path GFAffix/Cargo.toml --release
# built binary is located at GFAffix/target/release/gfaffix
$ gfaffix --help
Discover and collapse walk-preserving shared affixes of a given variation graph.
Usage: gfaffix [OPTIONS] <GRAPH>
Arguments:
<GRAPH> graph in GFA1 format, supports compressed (.gz) input
Options:
-o, --output_refined <REFINED_GRAPH_OUT>
Write refined graph output (GFA1 format) to supplied file instead of stdout; if file name
ends with .gz, output will be compressed [default: ]
-t, --output_transformation <TRANSFORMATION_OUT>
Report original nodes and their corresponding walks in refined graph to supplied file
[default: ]
-c, --check_transformation
Verifies that the transformed parts of the graphs spell out the identical sequence as in the
original graph
-a, --output_affixes <AFFIXES_OUT>
Report identified affixes [default: ]
-x, --dont_collapse <NO_COLLAPSE_PATH>
Do not collapse nodes on a given paths/walks ("P"/"W" lines) that match given regular
expression [default: ]
-p, --threads <THREADS>
Run in parallel on N threads [default: 1]
-v, --verbose
Sets log level to debug
-h, --help
Print help
-V, --version
Print version
gfaffix -c examples/example1.gfa > example1.gfaffixed.gfa