{"id":13752306,"url":"https://github.com/lh3/bedtk","last_synced_at":"2025-10-04T08:56:01.587Z","repository":{"id":54186313,"uuid":"212413401","full_name":"lh3/bedtk","owner":"lh3","description":"A simple toolset for BED files (warning: CLI may change before bedtk becomes stable)","archived":false,"fork":false,"pushed_at":"2025-08-24T23:18:04.000Z","size":468,"stargazers_count":142,"open_issues_count":1,"forks_count":17,"subscribers_count":7,"default_branch":"master","last_synced_at":"2025-09-20T13:29:58.697Z","etag":null,"topics":["bioinformatics"],"latest_commit_sha":null,"homepage":"","language":"C","has_issues":true,"has_wiki":null,"has_pages":null,"mirror_url":null,"source_name":null,"license":"mit","status":null,"scm":"git","pull_requests_enabled":true,"icon_url":"https://github.com/lh3.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.txt","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,"zenodo":null}},"created_at":"2019-10-02T18:29:37.000Z","updated_at":"2025-09-09T09:10:54.000Z","dependencies_parsed_at":"2024-08-03T09:03:37.215Z","dependency_job_id":"8c0524b9-70a2-4b59-bfdb-f6ee526540a0","html_url":"https://github.com/lh3/bedtk","commit_stats":null,"previous_names":[],"tags_count":2,"template":false,"template_full_name":null,"purl":"pkg:github/lh3/bedtk","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fbedtk","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fbedtk/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fbedtk/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fbedtk/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lh3","download_url":"https://codeload.github.com/lh3/bedtk/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lh3%2Fbedtk/sbom","scorecard":null,"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":278289491,"owners_count":25962356,"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","status":"online","status_checked_at":"2025-10-04T02:00:05.491Z","response_time":63,"last_error":null,"robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":true,"can_crawl_api":true,"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"],"created_at":"2024-08-03T09:01:03.366Z","updated_at":"2025-10-04T08:56:01.541Z","avatar_url":"https://github.com/lh3.png","language":"C","funding_links":[],"categories":["Ranked by starred repositories"],"sub_categories":[],"readme":"## Getting Started\n\n```sh\n# compile and install\ngit clone https://github.com/lh3/bedtk\ncd bedtk \u0026\u0026 make\n# filter a BED or VCF file\n./bedtk flt test/test-anno.bed.gz test/test-iso.bed.gz\n./bedtk flt -v test/test-anno.bed.gz test/test-iso.bed.gz      # non-overlapping lines\n./bedtk flt -cw100 test/test-anno.bed.gz test/test-sub.vcf.gz  # with a window\n# intersect (no sorting needed; overlapping records allowed)\n./bedtk isec test/test-anno.bed.gz test/test-iso.bed.gz\n# compute the breadth of coverage\n./bedtk cov test/test-anno.bed.gz test/test-iso.bed.gz\n# sort a BED file\n./bedtk sort test/test-iso.bed.gz\n./bedtk sort -s test/chr_list.txt test/test-iso.bed.gz\n# merge overlapping records (no sorting needed)\n./bedtk merge test/test-anno.bed.gz\n```\n\n## Introduction\n\nBedtk is a set of simple tools to process BED files. It so far implements\nintersection, subtraction, sorting, merging and computing the breadth of\ncoverage. Bedtk is not as versatile as [bedtools][bedtools] and never aims to\nmatch the bedtools feature set. It instead focuses on performance. Bedtk\nis several to tens of times faster and uses a fraction of memory. It also\nprovides a few convenient functions. For example, sorting, merging and\nintersection can be done in one go without Unix pipes.\n\nBedtk is published in:\n\u003e Li H and Rong J (2021) Bedtk: finding interval overlap with implicit interval tree.\n\u003e *Bioinformatics*, **37**:1315-1316\n\n[bedtools]: https://github.com/arq5x/bedtools2\n[cr]: https://github.com/lh3/cgranges\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flh3%2Fbedtk","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flh3%2Fbedtk","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flh3%2Fbedtk/lists"}