A tools to convert a list of kmer with count (in csv format) as kff file with minimizer compression
cargo install --git https://github.com/Kmer-File-Format/kmers2kff.git
mkdir tmp/
kmers2kff -i <input.csv> -o <output.kff> -k <kmer-size> -m <minimizer-size> -p tmp
rm tmp/
Kmer size must be lower than 65, minimizer size must be lower than kmer size.
By default csv delimiter is comma if you want use tabulation call with -d $'\t'.
Warning kmers2kff writes temporary files with a name like {prefix}{a number} if you run several kmers2kff at the same time be careful that their prefix is different to avoid collision between temporary files.
If RUST_LOG is set with info value kmers2kff write some log in stderr.
Complete cli:
kmers2kff 0.1
Pierre Marijon <pierre.marijon@hhu.de>
Convert a raw kmer count in kff format with a minimizer compression
USAGE:
kmers2kff [OPTIONS] --input <input> --output <output> --kmer-size <k> --minimizer-size <m> --prefix <prefix>
FLAGS:
-h, --help Prints help information
-V, --version Prints version information
OPTIONS:
-d, --delimiter <delimiter> Set delimiter between kmer and count in input [default: ,]
-i, --input <input> Path of kmers counts in csv format
-k, --kmer-size <k> Kmer size
-m, --minimizer-size <m> Minimizer size
-o, --output <output> Path of the kff file
-p, --prefix <prefix> Prefix add before temporary file
git clone https://github.com/Kmer-File-Format/kmers2kff.git
cd kmers2kff
cargo build [--release]
You can create pull request but before please run this command:
cargo test
cargo fmt
cargo clippy -- -D warnings
cargo test
All this command must finish without error.
Currently the minimum supported Rust version is 1.47.0.