{"id":26880110,"url":"https://github.com/sstadick/scivs","last_synced_at":"2025-03-31T13:34:48.175Z","repository":{"id":57734890,"uuid":"232199957","full_name":"sstadick/scivs","owner":"sstadick","description":"Collection of Data Structures for working with genomic intervals","archived":false,"fork":false,"pushed_at":"2020-06-09T12:48:52.000Z","size":33,"stargazers_count":2,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-03-27T04:09:31.384Z","etag":null,"topics":["algorithm","bioinformatics","scala","scala-port"],"latest_commit_sha":null,"homepage":"","language":"Scala","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/sstadick.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":"2020-01-06T22:55:00.000Z","updated_at":"2021-07-17T20:29:35.000Z","dependencies_parsed_at":"2022-08-24T11:20:33.696Z","dependency_job_id":null,"html_url":"https://github.com/sstadick/scivs","commit_stats":null,"previous_names":[],"tags_count":0,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sstadick%2Fscivs","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sstadick%2Fscivs/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sstadick%2Fscivs/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/sstadick%2Fscivs/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/sstadick","download_url":"https://codeload.github.com/sstadick/scivs/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":246474953,"owners_count":20783578,"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":["algorithm","bioinformatics","scala","scala-port"],"created_at":"2025-03-31T13:34:47.439Z","updated_at":"2025-03-31T13:34:48.129Z","avatar_url":"https://github.com/sstadick.png","language":"Scala","readme":"[![Latest version](https://index.scala-lang.org/sstadick/scivs/scivs/latest.svg)](https://index.scala-lang.org/sstadick/scivs/scivs)\n\n# scivs \n\nThis is a library containing Classes and helpers for working with\ngenomic intervals in Scala. Currently `Lapper` and `ScAIList` are\nimplemented, which are best in class in their respective niche's.\n\nscivs = SCala InterVal Stores\n\n## Lapper\n\nThis is a Scala port of the\n[nim-lapper](https://github.com/brentp/nim-lapper). It is also inspired\nby the rust port [rust-lapper](https://docs.rs/rust-lapper). \n\n```scala\nimport scivs.scailist.ScAIList\nimport scivs.interval.Interval\nval lapper = new Lapper((0 to 20 by 5).map(Interval(_, _ + 2, 0)).toList))\nassert(lapper.find(6, 11).toList(0), Interval(5, 7, 0))\n```\n\n### Performance Characteristics\n\nFantastic for 'normal' genomic data where intervals are 'short' and\nthere isn't much nesting. Think Illumina PE reads. The `seek` method in\nparticular is very fast if you know that your queries will be in order.\n\n## ScAIList\n\nThis is an implementation of the code from this\n[paper](https://www.biorxiv.org/content/10.1101/593657v1). The major\nchange is that the number of component parts a list is broken into is\ndynamic and not hardcoded. \n\n### Performance Characteristics\n\nThis datastructure is good for nested intervals where long intervals\nengulf many shorter intervals. \n\n```scala\nimport scivs.scailist.ScAIList\nimport scivs.interval.Interval\nval scailist = ScAIList((0 to 20 by 5).map(Interval(_, _ + 2, 0)).toList))\nassert(scailist.find(6, 11).toList(0), Interval(5, 7, 0))\n```\n\n\n## Todo's\n\n- Add benchmarks / substantiate the performance characteristics\n- Compare against other libs out there?\n- Add some of the helper methods for things like coverage etc\n- Figure out how to make my package level docs show up in javadoc\n","funding_links":[],"categories":[],"sub_categories":[],"project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsstadick%2Fscivs","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fsstadick%2Fscivs","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fsstadick%2Fscivs/lists"}