{"id":17220825,"url":"https://github.com/kojix2/ruby-edlib","last_synced_at":"2025-04-13T23:46:48.774Z","repository":{"id":62312694,"uuid":"559318048","full_name":"kojix2/ruby-edlib","owner":"kojix2","description":"ruby-edlib is a wrapper for edlib","archived":false,"fork":false,"pushed_at":"2025-01-17T03:35:49.000Z","size":159,"stargazers_count":2,"open_issues_count":1,"forks_count":1,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-03-27T13:51:23.807Z","etag":null,"topics":["bioinformatics","edlib","ruby"],"latest_commit_sha":null,"homepage":"https://kojix2.github.io/ruby-edlib/","language":"C++","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"other","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/kojix2.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":".github/FUNDING.yml","license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null},"funding":{"ko_fi":"kojix2"}},"created_at":"2022-10-29T18:32:47.000Z","updated_at":"2025-01-17T03:35:39.000Z","dependencies_parsed_at":"2024-02-10T01:29:45.392Z","dependency_job_id":"6a87a1ef-5d85-460b-bd67-6c546f9aca0f","html_url":"https://github.com/kojix2/ruby-edlib","commit_stats":{"total_commits":62,"total_committers":1,"mean_commits":62.0,"dds":0.0,"last_synced_commit":"472a155ebcfcfdf184904105d188a5702a1c0a59"},"previous_names":[],"tags_count":10,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kojix2%2Fruby-edlib","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kojix2%2Fruby-edlib/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kojix2%2Fruby-edlib/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/kojix2%2Fruby-edlib/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/kojix2","download_url":"https://codeload.github.com/kojix2/ruby-edlib/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248799697,"owners_count":21163398,"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":["bioinformatics","edlib","ruby"],"created_at":"2024-10-15T03:53:20.229Z","updated_at":"2025-04-13T23:46:48.747Z","avatar_url":"https://github.com/kojix2.png","language":"C++","funding_links":["https://ko-fi.com/kojix2"],"categories":[],"sub_categories":[],"readme":"# ruby-edlib\n\n[![Gem Version](https://badge.fury.io/rb/edlib.svg)](https://badge.fury.io/rb/edlib)\n[![test](https://github.com/kojix2/ruby-edlib/actions/workflows/ci.yml/badge.svg)](https://github.com/kojix2/ruby-edlib/actions/workflows/ci.yml)\n[![DOI](https://zenodo.org/badge/559318048.svg)](https://zenodo.org/badge/latestdoi/559318048)\n\n[Edlib](https://github.com/Martinsos/edlib) - A lightweight and super fast C/C++ library for sequence alignment using edit distance\n\n## Installation\n\n```\ngem install edlib\n```\n\nThe Gem compiles the edlib source code inside the gem at installation. If you want to use the latest edlib, see Development.\n\n## Usage\n\n```ruby\nrequire \"edlib\"\n\na = Edlib::Aligner.new(mode: :hw, task: :path)\na.align(\"AACG\", \"TCAACCTG\")\n\n# {\n#  :edit_distance   =\u003e 1,\n#  :alphabet_length =\u003e 4,\n#  :locations       =\u003e [[2, 4], [2, 5]],\n#  :alignment       =\u003e [0, 0, 0, 1],\n#  :cigar           =\u003e \"3=1I\"\n# }\n```\n\n|keyword argument     |description|\n|---------------------|-----------------------------------------------------------------------------|\n|k                    |edit distance is not larger than k [-1]                                             |\n|mode                 |global (NW) , prefix (SHW) , infix (HW) [\"NW\"]                                      |\n|task                 |DISTANCE, LOC, PATH [\"DISTANCE\"]                                                    |\n|additional_equalities|List of pairs of characters, where each pair defines two characters as equal. [NULL]|\n\n\n```ruby\na.align(\"AACG\", \"TCAACCTG\", nice: true)\n\n# {\n#   :edit_distance=\u003e1,                                                 \n#   :alphabet_length=\u003e4,                                               \n#   :locations=\u003e[[2, 4], [2, 5]],                                      \n#   :alignment=\u003e[0, 0, 0, 1],                                          \n#   :cigar=\u003e\"3=1I\",                                                    \n#   :query_aligned=\u003e\"AACG\",                                            \n#   :match_aligned=\u003e\"|||-\",                                            \n#   :target_aligned=\u003e\"AAC-\"\n# }        \n```\n\n## Documentation\n\nhttps://kojix2.github.io/ruby-edlib/\n\n## Development\n\nPull requests welcome!\n\n```sh\ngit clone https://github.com/kojix2/ruby-edlib # Please fork repo\ncd ruby-edlib\nbundle install\nbundle exec rake compile\nbundle exec rake test\n```\n\nUse latest edlib\n\n```sh\ngit clone https://github.com/kojix2/ruby-edlib\ncd ruby-edlib\nbundle install\nbundle exec rake edlib:update # Download latest edlib.h and edlib.cpp\nbundle exec rake compile\nbundle exec rake test\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkojix2%2Fruby-edlib","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fkojix2%2Fruby-edlib","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fkojix2%2Fruby-edlib/lists"}