Zoe provides both broad and highly specialized implementations for bioinformatics. In particular, we focus on common data formats and methods relevant for the sequencing of RNA viruses. Read the documentation.
This library runs on Rust nightly.
Zoe has design goals that may or may not be compatible with your project:
- Embracing Rust Nightly to enable early access to features and fixes, especially portable SIMD
- Providing broad support for the authors' activities over creating a multiplicity of smaller projects.
- Avoiding
unsafeas well as non-portable implementations - Avoiding large transitive dependency trees and binary sizes
- Providing reasonably performant solutions while not sacrificing the above
- Porting diverse, relevant methods and providing clear attribution to the original authors
If you would like to pin to a Github tag or commit, you could use the following within your Cargo.toml project file:
[dependencies]
# Fill in VERSION_TAG_HERE with tagged version:
zoe = { git = "https://github.com/CDCgov/zoe", tag = "VERSION_TAG_HERE"}
# OR, fill in MAIN_COMMIT_HERE:
zoe = { git = "https://github.com/CDCgov/zoe", commit = "MAIN_COMMIT_HERE"}CAUTION: because feature branches get routinely deleted, pinning to feature branches (via branch, commit or tag) should only be used for active development or forks!
Zoe has used a number of nightly features over its lifetime. Some have been stabilized (e.g., lazy_cell,const_fn_floating_point_arithmetic) while others have been removed (iter_collect_into), avoided (array_chunks, iter_array_chunks), or forbidden due to incompleteness (generic_const_exprs).
In order for Zoe to move to stable, the portable SIMD nightly feature would first need to be stabilized since it is an essential component of the library. After that, Zoe could march towards stable Rust by gating, working around or removing any remaining nightly features. Notwithstanding, development of Zoe is likely to continue on nightly, if only for convenient access to nightly bencher, the latest LLVM code generation, and convenient use of rustfmt's unstable features.
This list may not be up-to-date or exhaustive, but some example usage:
- Alignment functions: [
alignment::sw::sw_simd_score] - Composition functions: [
composition::gc_content_simd], [composition::AlignmentComposition] - Distance functions: [
distance::hamming_simd], [distance::dna::p_distance_acgt] - Search
- Substring: [
search::fuzzy_substring_match_simd], [search::substring_match_simd], [search::find_k_repeating] - Byte: [
search::position_by_byte] (and other variants) and [search::replace_all_bytes_simd]
- Substring: [
- Transformation functions: [
data::types::nucleotides::reverse_complement_simd] - Validation functions: [
data::CheckSequence]
While it is always welcome to cite Zoe as the implementation (see CITATION.bib)for the method being used. To that end, the innermost function (not convenience methods) usually contains all relevant citations to it (raise an issue if not). In addition, the complete bibliography of methods used in this library is included in BibTex format for easy inclusion in a mansuscript (see BIBLIOGRAPHY.bib).
Zoe is designed to minimize large dependency trees and binary sizes while providing performant solutions. Several dependencies are optional and can be enabled as features at the user's discretion.
- rand: Enabled by default. This optional feature provides support for random sequence generation for nucleotides and amino acids. Adds the dependency rand_xoshiro.
- multiversion: This optional feature adds multiversioning of select Zoe SIMD functions using the multiversion crate.
- arbitrary: This optional feature adds
Arbitraryimplementations to many of Zoe's data types to support fuzz testing. It also introduces many wrapper types with customArbitraryimplementations providing data with stronger assumptions. See TODO for more details.
For direct correspondence on the project, feel free to contact: Samuel S. Shepard, Centers for Disease Control and Prevention or reach out to other contributors.
This repository constitutes a work of the United States Government and is not subject to domestic copyright protection under 17 USC § 105. This repository is in the public domain within the United States, and copyright and related rights in the work worldwide are waived through the CC0 1.0 Universal public domain dedication. All contributions to this repository will be released under the CC0 dedication. By submitting a pull request you are agreeing to comply with this waiver of copyright interest.
The repository utilizes code licensed under the terms of the Apache Software License and therefore is licensed under ASL v2 or later. This source code in this repository is free: you can redistribute it and/or modify it under the terms of the Apache Software License version 2, or (at your option) any later version. This source code in this repository is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the Apache Software License for more details. You should have received a copy of the Apache Software License along with this program. If not, see: http://www.apache.org/licenses/LICENSE-2.0.html. The source code forked from other open source projects will inherit its license.
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