{"id":33933493,"url":"https://github.com/informationsea/vcf-rs","last_synced_at":"2026-04-07T15:31:09.278Z","repository":{"id":57671492,"uuid":"248002958","full_name":"informationsea/vcf-rs","owner":"informationsea","description":"Rust implmentation of VCF parser","archived":false,"fork":false,"pushed_at":"2022-10-02T11:08:22.000Z","size":39002,"stargazers_count":25,"open_issues_count":1,"forks_count":2,"subscribers_count":2,"default_branch":"master","last_synced_at":"2025-12-13T23:43:36.807Z","etag":null,"topics":["bioinformatics","parser","rust"],"latest_commit_sha":null,"homepage":null,"language":"Rust","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/informationsea.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":"2020-03-17T15:18:26.000Z","updated_at":"2025-10-10T17:57:50.000Z","dependencies_parsed_at":"2022-09-26T20:41:20.449Z","dependency_job_id":null,"html_url":"https://github.com/informationsea/vcf-rs","commit_stats":null,"previous_names":[],"tags_count":6,"template":false,"template_full_name":null,"purl":"pkg:github/informationsea/vcf-rs","repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/informationsea%2Fvcf-rs","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/informationsea%2Fvcf-rs/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/informationsea%2Fvcf-rs/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/informationsea%2Fvcf-rs/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/informationsea","download_url":"https://codeload.github.com/informationsea/vcf-rs/tar.gz/refs/heads/master","sbom_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/informationsea%2Fvcf-rs/sbom","scorecard":{"id":488368,"data":{"date":"2025-08-11","repo":{"name":"github.com/informationsea/vcf-rs","commit":"4670879711c2588cd6d3f0ffaf78303ebbbef35e"},"scorecard":{"version":"v5.2.1-40-gf6ed084d","commit":"f6ed084d17c9236477efd66e5b258b9d4cc7b389"},"score":3.4,"checks":[{"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":"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":"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":"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":"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/build.yml:42: update your workflow using https://app.stepsecurity.io/secureworkflow/informationsea/vcf-rs/build.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/build.yml:49: update your workflow using https://app.stepsecurity.io/secureworkflow/informationsea/vcf-rs/build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/build.yml:56: update your workflow using https://app.stepsecurity.io/secureworkflow/informationsea/vcf-rs/build.yml/master?enable=pin","Warn: GitHub-owned GitHubAction not pinned by hash: .github/workflows/build.yml:65: update your workflow using https://app.stepsecurity.io/secureworkflow/informationsea/vcf-rs/build.yml/master?enable=pin","Warn: third-party GitHubAction not pinned by hash: .github/workflows/build.yml:75: update your workflow using https://app.stepsecurity.io/secureworkflow/informationsea/vcf-rs/build.yml/master?enable=pin","Info:   0 out of   3 GitHub-owned GitHubAction dependencies pinned","Info:   0 out of   2 third-party GitHubAction 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":"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/build.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":"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":"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":"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":"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":"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":"License","score":10,"reason":"license file detected","details":["Info: project has a license file: LICENSE:0","Info: FSF or OSI recognized license: Apache License 2.0: LICENSE:0"],"documentation":{"short":"Determines if the project has defined a license.","url":"https://github.com/ossf/scorecard/blob/f6ed084d17c9236477efd66e5b258b9d4cc7b389/docs/checks.md#license"}},{"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":"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":"2025-08-19T18:24:49.520Z","repository_id":57671492,"created_at":"2025-08-19T18:24:49.520Z","updated_at":"2025-08-19T18:24:49.520Z"},"host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":286080680,"owners_count":31518394,"icon_url":"https://github.com/github.png","version":null,"created_at":"2022-05-30T11:31:42.601Z","updated_at":"2026-04-07T03:10:19.677Z","status":"ssl_error","status_checked_at":"2026-04-07T03:10:13.982Z","response_time":105,"last_error":"SSL_connect returned=1 errno=0 peeraddr=140.82.121.5:443 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","parser","rust"],"created_at":"2025-12-12T13:04:26.767Z","updated_at":"2026-04-07T15:31:09.266Z","avatar_url":"https://github.com/informationsea.png","language":"Rust","funding_links":[],"categories":[],"sub_categories":[],"readme":"vcf-rs\r\n======\r\n[![Build](https://github.com/informationsea/vcf-rs/actions/workflows/build.yml/badge.svg)](https://github.com/informationsea/vcf-rs/actions/workflows/build.yml)\r\n[![Crates.io](https://img.shields.io/crates/v/vcf)](https://crates.io/crates/vcf)\r\n[![doc-rs](https://docs.rs/vcf/badge.svg)](https://docs.rs/vcf)\r\n[![GitHub](https://img.shields.io/github/license/informationsea/vcf-rs)](https://github.com/informationsea/vcf-rs)\r\n[![GitHub top language](https://img.shields.io/github/languages/top/informationsea/vcf-rs)](https://github.com/informationsea/vcf-rs)\r\n\r\nRust implementation of VCF parser.\r\n\r\nLicense\r\n-------\r\nApache 2.0\r\n\r\n\r\nExample\r\n-------\r\n\r\n```rust\r\nuse vcf::*;\r\nuse flate2::read::MultiGzDecoder;\r\nuse std::fs::File;\r\n\r\nfn usage_test() -\u003e Result\u003c(), VCFError\u003e {\r\n    let mut reader = VCFReader::new(BufReader::new(MultiGzDecoder::new(File::open(\r\n        \"./testfiles/NA12878-subset.vcf.gz\",\r\n    )?)))?;\r\n\r\n    // access FILTER contents\r\n    assert_eq!(\r\n        Some(VCFHeaderFilterAlt {\r\n            id: b\"PASS\",\r\n            description: b\"All filters passed\"\r\n        }),\r\n        reader.header().filter(b\"PASS\")\r\n    );\r\n\r\n    // access INFO contents\r\n    assert_eq!(\r\n        b\"Stop position of the interval\",\r\n        reader.header().info(b\"END\").unwrap().description\r\n    );\r\n\r\n    // prepare VCFRecord object\r\n    let mut vcf_record = VCFRecord::new(reader.header());\r\n\r\n    // read one record\r\n    reader.next_record(\u0026mut vcf_record)?;\r\n\r\n    // get record attributes\r\n    assert_eq!(vcf_record.chromosome, b\"13\");\r\n    assert_eq!(vcf_record.position, 32889968);\r\n    assert_eq!(vcf_record.id, Vec::\u003cU8Vec\u003e::new());\r\n    assert_eq!(vcf_record.reference, b\"G\");\r\n    assert_eq!(vcf_record.alternative, vec![b\"A\"]);\r\n    assert_eq!(vcf_record.qual, Some(25743.5));\r\n    assert_eq!(vcf_record.info(b\"AC\"), Some(\u0026vec![b\"54\".to_vec()]));\r\n    assert_eq!(\r\n        vcf_record.genotype(b\"ERP001775_HiSeq2000_SAMEA1531955-1\", b\"GT\"),\r\n        Some(\u0026vec![b\"1/1\".to_vec()])\r\n    );\r\n    assert_eq!(\r\n        vcf_record.genotype(b\"ERP001775_HiSeq2000_SAMEA1531955-1\", b\"AD\"),\r\n        Some(\u0026vec![b\"0\".to_vec(), b\"14\".to_vec()])\r\n    );\r\n\r\n    Ok(())\r\n}\r\n```","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finformationsea%2Fvcf-rs","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Finformationsea%2Fvcf-rs","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Finformationsea%2Fvcf-rs/lists"}