{"id":19909675,"url":"https://github.com/chrovis/clj-bwa","last_synced_at":"2025-07-05T16:41:17.033Z","repository":{"id":19355450,"uuid":"22595029","full_name":"chrovis/clj-bwa","owner":"chrovis","description":"Burrows-Wheeler Aligner (BWA) wrapper for Clojure","archived":false,"fork":false,"pushed_at":"2016-02-10T07:43:39.000Z","size":178,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":10,"default_branch":"master","last_synced_at":"2025-03-01T08:25:40.133Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"language":"Clojure","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"apache-2.0","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/chrovis.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2014-08-04T07:01:37.000Z","updated_at":"2017-04-21T01:51:35.000Z","dependencies_parsed_at":"2022-09-10T20:31:19.306Z","dependency_job_id":null,"html_url":"https://github.com/chrovis/clj-bwa","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"purl":"pkg:github/chrovis/clj-bwa","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fclj-bwa","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fclj-bwa/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fclj-bwa/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fclj-bwa/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/chrovis","download_url":"https://codeload.github.com/chrovis/clj-bwa/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/chrovis%2Fclj-bwa/sbom","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":263773158,"owners_count":23509209,"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":[],"created_at":"2024-11-12T21:16:19.211Z","updated_at":"2025-07-05T16:41:17.014Z","avatar_url":"https://github.com/chrovis.png","language":"Clojure","funding_links":[],"categories":[],"sub_categories":[],"readme":"clj-bwa\n=======\n\nclj-bwa is Burrows-Wheeler Aligner (BWA) wrapper for Clojure.\n\n[![Build Status](https://travis-ci.org/chrovis/clj-bwa.svg?branch=master)](https://travis-ci.org/chrovis/clj-bwa)\n\nRequirements\n------------\n\n- [libbwa][libbwa]\n\nclj-bwa uses libbwa native library via Java Native Access (JNA).\nInstall libbwa to system or locate it on your `java.library.path`.\n\nUsage\n-----\n\nAdd the following dependency to your project.clj.\n\n```clojure\n[clj-bwa \"0.1.0-SNAPSHOT\"]\n```\n\nclj-bwa wraps BWA sub-commands for calling its features from Clojure codes.\n\n```clojure\n(require '[clj-bwa.core :as bwa])\n\n;; Index database sequences in the FASTA format.\n(bwa/index \"path/to/reference.fa\" \"path/to/reference.fa\" :auto false)\n\n;; Align 70bp-1Mbp query sequences with the BWA-MEM algorithm.\n(let [opt (bwa/mem-option)]\n  (bwa/mem \"path/to/reference.fa\" \"path/to/read.fq\" nil \"path/to/out.sam\" opt)\n```\n\n## Development\n\n### Test\n\nTo run all tests,\n\n```bash\n$ lein midje\n```\n\n### Generating document\n\ncljam uses [Marginalia][marginalia] for generating documents.\n\n```bash\n$ lein marg -m\n```\n\ngenerates HTML documents in `docs` directory.\n\nLicense\n-------\n\nCopyright 2014 [Xcoo, Inc.][xcoo]\n\nLicensed under the [Apache License, Version 2.0][apache-license-2.0].\n\n[libbwa]: https://github.com/chrovis/libbwa\n[marginalia]: http://gdeer81.github.io/marginalia/\n[xcoo]: http://www.xcoo.jp\n[apache-license-2.0]: http://www.apache.org/licenses/LICENSE-2.0.html\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchrovis%2Fclj-bwa","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fchrovis%2Fclj-bwa","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fchrovis%2Fclj-bwa/lists"}