{"id":25596842,"url":"https://github.com/nanoporetech/bripy","last_synced_at":"2025-06-15T19:09:17.510Z","repository":{"id":57416386,"uuid":"226492062","full_name":"nanoporetech/bripy","owner":"nanoporetech","description":"Bam Read Index for python","archived":false,"fork":false,"pushed_at":"2019-12-07T10:20:37.000Z","size":143,"stargazers_count":4,"open_issues_count":1,"forks_count":0,"subscribers_count":17,"default_branch":"master","last_synced_at":"2025-04-06T08:02:14.507Z","etag":null,"topics":[],"latest_commit_sha":null,"homepage":null,"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/nanoporetech.png","metadata":{"files":{"readme":"README.md","changelog":null,"contributing":null,"funding":null,"license":"LICENSE.md","code_of_conduct":null,"threat_model":null,"audit":null,"citation":null,"codeowners":null,"security":null,"support":null}},"created_at":"2019-12-07T10:18:26.000Z","updated_at":"2024-12-10T07:40:45.000Z","dependencies_parsed_at":"2022-09-26T20:11:43.565Z","dependency_job_id":null,"html_url":"https://github.com/nanoporetech/bripy","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/nanoporetech%2Fbripy","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Fbripy/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Fbripy/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/nanoporetech%2Fbripy/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/nanoporetech","download_url":"https://codeload.github.com/nanoporetech/bripy/tar.gz/refs/heads/master","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":248657795,"owners_count":21140841,"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":"2025-02-21T12:34:43.546Z","updated_at":"2025-04-13T02:31:01.534Z","avatar_url":"https://github.com/nanoporetech.png","language":"C","funding_links":[],"categories":[],"sub_categories":[],"readme":"\n![Oxford Nanopore Technologies logo](https://github.com/nanoporetech/bripy/raw/master/images/ONT_logo_590x106.png)\n\n\nBripy\n======\n\nBripy is a python library for extracting reads from a bam by read name. It\nuses the [bri](https://github.com/jts/bri) library from Jared Simpson.\n\n© 2019 Oxford Nanopore Technologies Ltd.\n\nInstallation\n------------\n\n`bripy` can be installed using pip:\n\n    pip install bripy\n\nFor python3.5 and python3.6 under linux this will download precompiled\nbinaries, in other environments a source distribution will be downloaded\nand compiled. Compilation from source requires the same libraries as\n[htslib](https://github.com/samtools/htslib):\n\n    'm', 'z', 'lzma', 'bz2', 'pthread', 'curl', 'crypto'\n\nsince htslib is built from source as part of the process.\n\nUsage\n-----\n\nThe library contains a single class interface and two example programs. To\nindex a bam file for later retrieval of reads run:\n\n    bripy index \u003cbamfile\u003e\n\nThis program is analogous to the `bri index \u003cbamfile`. The second program\nwill retrieve reads from a bam by name:\n\n    bripy get \u003cbamfile\u003e \u003cread name\u003e\n\nAgain this program is analogous to running `bri get \u003cbamfile\u003e \u003cread name\u003e`.\n\nThe `bripy` API is simple, the following will return a string containing\nsam formatted alignments:\n\n    bri = BamReadIndex(bam_file)\n    sam_data = bri.get_alignments(read_name)\n\nThis API is likely to change in future to provide a more useful data structure\nakin to a `pysam.AlignedSegment`.\n\n\nLicense\n-------\n\n**Licence and Copyright**\n\n© 2019 Oxford Nanopore Technologies Ltd.\n\n`bripy` is distributed under the terms of the Mozilla Public License 2.0.\n\n**Research Release**\n\nResearch releases are provided as technology demonstrators to provide early\naccess to features or stimulate Community development of tools. Support for\nthis software will be minimal and is only provided directly by the developers.\nFeature requests, improvements, and discussions are welcome and can be\nimplemented by forking and pull requests. However much as we would\nlike to rectify every issue and piece of feedback users may have, the\ndevelopers may have limited resource for support of this software. Research\nreleases may be unstable and subject to rapid iteration by Oxford Nanopore\nTechnologies.\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnanoporetech%2Fbripy","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fnanoporetech%2Fbripy","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fnanoporetech%2Fbripy/lists"}