{"id":42433800,"url":"https://github.com/lemieuxl/pybgen","last_synced_at":"2026-01-28T04:56:56.703Z","repository":{"id":62578928,"uuid":"96350356","full_name":"lemieuxl/pybgen","owner":"lemieuxl","description":"Python module to process BGEN files as dosage data","archived":false,"fork":false,"pushed_at":"2024-02-14T14:42:08.000Z","size":7354,"stargazers_count":5,"open_issues_count":0,"forks_count":4,"subscribers_count":1,"default_branch":"master","last_synced_at":"2025-08-20T03:22:24.697Z","etag":null,"topics":["bioinformatics","genetics","genomics"],"latest_commit_sha":null,"homepage":"","language":"Python","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/lemieuxl.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}},"created_at":"2017-07-05T18:40:40.000Z","updated_at":"2022-05-06T15:38:47.000Z","dependencies_parsed_at":"2022-11-03T21:02:06.820Z","dependency_job_id":null,"html_url":"https://github.com/lemieuxl/pybgen","commit_stats":null,"previous_names":[],"tags_count":10,"template":false,"template_full_name":null,"purl":"pkg:github/lemieuxl/pybgen","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lemieuxl%2Fpybgen","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lemieuxl%2Fpybgen/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lemieuxl%2Fpybgen/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lemieuxl%2Fpybgen/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/lemieuxl","download_url":"https://codeload.github.com/lemieuxl/pybgen/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/lemieuxl%2Fpybgen/sbom","scorecard":{"id":583847,"data":{"date":"2025-08-11","repo":{"name":"github.com/lemieuxl/pybgen","commit":"56cc8a4afa0fe8d7c214e054226db0c3ee60165d"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":3.4,"checks":[{"name":"Packaging","score":-1,"reason":"packaging workflow not detected","details":["Warn: no GitHub/GitLab publishing workflow detected."],"documentation":{"short":"Determines if the project is published as a package that others can easily download, install, easily update, and uninstall.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#packaging"}},{"name":"Token-Permissions","score":0,"reason":"detected GitHub workflow tokens with excessive permissions","details":["Warn: no topLevel permission defined: .github/workflows/python-app.yml:1","Info: no jobLevel write permissions found"],"documentation":{"short":"Determines if the project's workflows follow the principle of least privilege.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#token-permissions"}},{"name":"Binary-Artifacts","score":10,"reason":"no binaries found in the repo","details":null,"documentation":{"short":"Determines if the project has generated executable (binary) artifacts in the source repository.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#binary-artifacts"}},{"name":"SAST","score":0,"reason":"no SAST tool detected","details":["Warn: no pull requests merged into dev branch"],"documentation":{"short":"Determines if the project uses static code analysis.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#sast"}},{"name":"Dangerous-Workflow","score":10,"reason":"no dangerous workflow patterns detected","details":null,"documentation":{"short":"Determines if the project's GitHub Action workflows avoid dangerous patterns.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#dangerous-workflow"}},{"name":"Code-Review","score":0,"reason":"Found 0/30 approved changesets -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project requires human code review before pull requests (aka merge requests) are merged.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#code-review"}},{"name":"Maintained","score":0,"reason":"0 commit(s) and 0 issue activity found in the last 90 days -- score normalized to 0","details":null,"documentation":{"short":"Determines if the project is \"actively maintained\".","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#maintained"}},{"name":"CII-Best-Practices","score":0,"reason":"no effort to earn an OpenSSF best practices badge detected","details":null,"documentation":{"short":"Determines if the project has an OpenSSF (formerly CII) Best Practices Badge.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#cii-best-practices"}},{"name":"Security-Policy","score":0,"reason":"security policy file not detected","details":["Warn: no security policy file detected","Warn: no security file to analyze","Warn: no security file to analyze","Warn: no security file to analyze"],"documentation":{"short":"Determines if the project has published a security policy.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#security-policy"}},{"name":"Pinned-Dependencies","score":0,"reason":"dependency not pinned by hash detected -- score normalized to 0","details":["Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/python-app.yml:18: update your workflow using https://app.stepsecurity.io/secureworkflow/lemieuxl/pybgen/python-app.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/python-app.yml:21: update your workflow using https://app.stepsecurity.io/secureworkflow/lemieuxl/pybgen/python-app.yml/master?enable=pin","Warn: pipCommand not pinned by hash: .github/workflows/python-app.yml:27","Warn: pipCommand not pinned by hash: .github/workflows/python-app.yml:28","Info:   0 out of   2 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   2 pipCommand dependencies pinned"],"documentation":{"short":"Determines if the project has declared and pinned the dependencies of its build process.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#pinned-dependencies"}},{"name":"Vulnerabilities","score":10,"reason":"0 existing vulnerabilities detected","details":null,"documentation":{"short":"Determines if the project has open, known unfixed vulnerabilities.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#vulnerabilities"}},{"name":"Signed-Releases","score":-1,"reason":"no releases found","details":null,"documentation":{"short":"Determines if the project cryptographically signs release artifacts.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#signed-releases"}},{"name":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE.txt:0","Info: FSF or OSI recognized license: MIT License: LICENSE.txt:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"name":"Fuzzing","score":0,"reason":"project is not fuzzed","details":["Warn: no fuzzer integrations found"],"documentation":{"short":"Determines if the project uses fuzzing.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#fuzzing"}},{"name":"Branch-Protection","score":0,"reason":"branch protection not enabled on development/release branches","details":["Warn: branch protection not enabled for branch 'master'"],"documentation":{"short":"Determines if the default and release branches are protected with GitHub's branch protection settings.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#branch-protection"}}]},"last_synced_at":"2025-08-20T19:54:35.577Z","repository_id":62578928,"created_at":"2025-08-20T19:54:35.578Z","updated_at":"2025-08-20T19:54:35.578Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":28839503,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-01-28T02:10:51.810Z","status":"ssl_error","status_checked_at":"2026-01-28T02:10:50.806Z","response_time":57,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.6:443 state=error: unexpected eof while reading","robots_txt_status":"success","robots_txt_updated_at":"2025-07-24T06:49:26.215Z","robots_txt_url":"https://github.com/robots.txt","online":false,"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","genetics","genomics"],"created_at":"2026-01-28T04:56:56.142Z","updated_at":"2026-01-28T04:56:56.698Z","avatar_url":"https://github.com/lemieuxl.png","language":"Python","funding_links":[],"categories":[],"sub_categories":[],"readme":"# pybgen - Module to process BGEN files\n\n[![Build Status](https://github.com/lemieuxl/pybgen/actions/workflows/python-app.yml/badge.svg?branch=master)](https://github.com/lemieuxl/pybgen/actions)\n[![PyPI version](https://badgen.net/pypi/v/pybgen)](https://pypi.org/project/pybgen/)\n\n`PyBGEN` is a Python module to read and write BGEN binary files and extract\ndosage data.\n\nA short documentation is available at\n[https://lemieuxl.github.io/pybgen/](https://lemieuxl.github.io/pybgen/).\n\n## Dependencies\n\nThe tool requires a standard [Python](http://python.org/) installation (2.7 and\n3.6 or higher are supported) with the following modules:\n\n1. [numpy](http://www.numpy.org/) version 1.12.0 or latest\n2. [six](https://pythonhosted.org/six/) version 1.10.0 or latest\n\nThe tool has been tested on *Linux*, but should work on *MacOS* and *Windows*\noperating systems as well.\n\n## Installation\n\nUsing `pip`:\n\n```bash\npip install pybgen\n```\n\nUsing `conda`:\n\n```bash\nconda install pybgen -c http://statgen.org/wp-content/uploads/Softwares/pybgen\n```\n\nIt is possible to add the channel to conda's configuration, so that the\n`-c http://statgen.org/...` can be omitted to update or install the package.\nTo add the channel, perform the following command:\n\n```bash\nconda config --add channels http://statgen.org/wp-content/uploads/Softwares/pybgen\n```\n\n### Updating\n\nTo update the module using `pip`:\n\n```bash\npip install -U pybgen\n```\n\nTo update the module using `conda`:\n\n```bash\n# If the channel has been configured (see above)\nconda update pybgen\n\n# Otherwise\nconda update pybgen -c http://statgen.org/wp-content/uploads/Softwares/pybgen\n```\n\n## Testing\n\nTo test the module, just perform the following command:\n\n```console\n$ python -m pybgen.tests\n......................................................................\n......................................................................\n......................................................................\n......................................................................\n......................................................................\n......................................................................\n......................................................................\n......................................\n----------------------------------------------------------------------\nRan 528 tests in 13.171s\n\nOK\n```\n","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flemieuxl%2Fpybgen","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Flemieuxl%2Fpybgen","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Flemieuxl%2Fpybgen/lists"}