{"id":24995133,"url":"https://github.com/louisaslett/kalis","last_synced_at":"2025-04-12T04:10:29.964Z","repository":{"id":183769512,"uuid":"88178476","full_name":"louisaslett/kalis","owner":"louisaslett","description":"kalis: High Performance Li \u0026 Stephens Local Ancestry Inference","archived":false,"fork":false,"pushed_at":"2024-11-13T18:26:33.000Z","size":20584,"stargazers_count":8,"open_issues_count":0,"forks_count":1,"subscribers_count":3,"default_branch":"master","last_synced_at":"2025-03-25T23:41:44.104Z","etag":null,"topics":["genetics","genomics","hpc-applications","r"],"latest_commit_sha":null,"homepage":"https://kalis.louisaslett.com/","language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":null,"status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/louisaslett.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":null,"code_of_conduct":null,"threat_model":null,"audit":null,"citation":"CITATION.cff","codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2017-04-13T15:16:43.000Z","updated_at":"2025-03-07T16:23:49.000Z","dependencies_parsed_at":null,"dependency_job_id":"cea67667-ee99-4f6d-ba24-818491502462","html_url":"https://github.com/louisaslett/kalis","commit_stats":null,"previous_names":["louisaslett/kalis"],"tags_count":1,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/louisaslett%2Fkalis","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/louisaslett%2Fkalis/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/louisaslett%2Fkalis/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/louisaslett%2Fkalis/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/louisaslett","download_url":"https://codeload.github.com/louisaslett/kalis/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248514221,"owners_count":21116903,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2022-07-04T15:15:14.044Z","host_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub","repositories_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories","repository_names_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repository_names","owners_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners"}},"keywords":["genetics","genomics","hpc-applications","r"],"created_at":"2025-02-04T15:34:04.579Z","updated_at":"2025-04-12T04:10:29.940Z","avatar_url":"https://github.com/louisaslett.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"# kalis: High Performance Li \u0026amp; Stephens Local Ancestry Inference\n\nkalis (doi: [10.1186/s12859-024-05688-8](https://doi.org/10.1186/s12859-024-05688-8)) provides a high performance implementation of the Li \u0026 Stephens model (doi: [10.1093/genetics/165.4.2213](https://doi.org/10.1093/genetics/165.4.2213)) for local ancestry inference (local referring to a region of the genome).\nFor a set of N phased haplotypes, kalis computes the posterior marginal probability of each haplotype copying every other haplotype by running N hidden Markov models in parallel.\nThis yields an N x N matrix that summarizes the recent local ancestry at each variant of interest.\nThe package provides functionality for specifying a recombination map, site-specific mutation rates, and differing prior copying probabilities for each recipient haplotype.\nExtensive use is made of low level threading and CPU vector instructions.\n\n## Installation\n\nkalis will appear on CRAN in due course.\nFor now, the current development version can be installed using the [remotes](https://github.com/r-lib/remotes) package as follows:\n\n```\ninstall.packages(\"remotes\")\nremotes::install_github(\"louisaslett/kalis\", build_vignettes = TRUE)\n```\n\nNote that kalis uses various low-level optimisations meaning that you should ensure the compiler is targeting your local CPU architecture.\nThe simplest way to do this is to pass configure variables setting the correct `CFLAGS` at install time:\n\n```\nremotes::install_github(\"louisaslett/kalis\",\n  configure.vars = c(kalis = \"PKG_CFLAGS='-march=native -mtune=native -O3'\"),\n  build_vignettes = TRUE)\n```\n\nIf you do not have the correct flags set, kalis will fall back to an implementation which does not use the special vector instruction set architecture of your CPU and will provide a warning when you load the package in your R session.\n\n## Citation\n\nIf you make use of this software, please cite the primary reference:\n\n\u003e Aslett L. J. M., Christ R. R. (2024). \"kalis: a modern implementation of the Li \u0026 Stephens model for local ancestry inference in R.\" _BMC Bioinformatics_, *25*(1), 1-18. [doi:10.1186/s12859-024-05688-8](https://doi.org/10.1186/s12859-024-05688-8\u003e).\n\nbibTeX:\n\n```\n@Article{,\n  title = {kalis: a modern implementation of the Li \u0026 Stephens model for local ancestry inference in R},\n  author = {Aslett, L. J. M. and Christ, R. R.},\n  journal = {BMC Bioinformatics},\n  year = {2024},\n  volume = {25},\n  number = {1},\n  pages = {1--18},\n  doi = {10.1186/s12859-024-05688-8}\n}\n```\n\nSome additional functions were added after the above publication to enable checkpointing and clade matrix construction, which are described in:\n\n\u003e Christ, R.R., Wang, X., Aslett, L.J.M., Steinsaltz, D. and Hall, I. (2024) \"Clade Distillation for Genome-wide Association Studies\", _bioRxiv 2024.09.30.615852_. [doi:10.1101/2024.09.30.615852](https://doi.org/10.1101/2024.09.30.615852).\n\nbibTeX:\n\n```\n@Article{,\n  title = {Clade Distillation for Genome-wide Association Studies},\n  author = {Christ, R. R. and Wang, X. and Aslett, L. J. M. and Steinsaltz, D. and Hall, I.},\n  journal = {bioRxiv},\n  year = {2024},\n  number = {2024.09.30.615852},\n  doi = {10.1101/2024.09.30.615852}\n}\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flouisaslett%2Fkalis","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flouisaslett%2Fkalis","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flouisaslett%2Fkalis/lists"}