├── .github └── workflows │ ├── clippy_check.yml │ ├── coverage.yml │ ├── pypi.yml │ └── rust_test.yml ├── .gitignore ├── CITATION.cff ├── CONTRIBUTING.md ├── Cargo.lock ├── Cargo.toml ├── LICENSE ├── README.md ├── composition ├── Cargo.toml └── src │ ├── cgr.rs │ ├── lib.rs │ ├── oligo.rs │ └── oligocgr.rs ├── conda ├── .gitignore ├── Cargo.toml ├── LICENSE ├── pykmertools.pyi ├── pyproject.toml └── src │ └── lib.rs ├── counter ├── Cargo.toml └── src │ └── lib.rs ├── coverage ├── Cargo.toml └── src │ └── lib.rs ├── kmer ├── Cargo.toml └── src │ ├── kmer.rs │ ├── kmer_minimisers.rs │ ├── lib.rs │ └── minimiser.rs ├── kmertools ├── Cargo.toml └── src │ ├── args.rs │ ├── lib.rs │ └── main.rs ├── ktio ├── Cargo.toml └── src │ ├── fops.rs │ ├── lib.rs │ ├── mmap.rs │ └── seq.rs ├── misc ├── Cargo.toml └── src │ ├── lib.rs │ └── minimisers.rs ├── pip ├── .gitignore ├── Cargo.toml ├── LICENSE ├── pykmertools.pyi ├── pyproject.toml └── src │ └── lib.rs ├── pybindings ├── .gitignore ├── Cargo.toml ├── pykmertools.pyi └── src │ ├── cgr.rs │ ├── kmer.rs │ ├── lib.rs │ ├── min.rs │ └── oligo.rs ├── tarpaulin.toml ├── test_data ├── .gitignore ├── computed_counts_acgt_test │ ├── temp_kmers.part_0_chunk_0 │ ├── temp_kmers.part_0_chunk_1 │ ├── temp_kmers.part_1_chunk_0 │ └── temp_kmers.part_1_chunk_1 ├── computed_counts_test │ ├── temp_kmers.part_0_chunk_0 │ ├── temp_kmers.part_0_chunk_1 │ ├── temp_kmers.part_1_chunk_0 │ └── temp_kmers.part_1_chunk_1 ├── expected_counts.part_0_chunk_0 ├── expected_counts.vectors ├── expected_counts_acgt_test.counts ├── expected_counts_test.counts ├── expected_counts_unnorm.vectors ├── expected_fa.kmers ├── expected_fa_batch_unnorm.kmers ├── expected_fa_header.kmers ├── expected_fq_cov.kmers ├── expected_minimisers ├── expected_reads.cgr ├── expected_reads.k4.cgr ├── expected_seq_minimisers ├── reads.fa ├── reads.fq └── reads.fq.gz └── tests ├── test_cgr.py ├── test_kmers.py ├── test_min.py ├── test_oligo.py └── test_utils.py 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