{"id":16618588,"url":"https://github.com/brentp/xvcf-rs","last_synced_at":"2025-10-29T19:31:47.593Z","repository":{"id":194075390,"uuid":"690058920","full_name":"brentp/xvcf-rs","owner":"brentp","description":"VCF/BCF [un]compressed [un]indexed","archived":false,"fork":false,"pushed_at":"2024-12-09T18:08:37.000Z","size":34,"stargazers_count":9,"open_issues_count":0,"forks_count":0,"subscribers_count":2,"default_branch":"main","last_synced_at":"2025-02-02T04:41:12.945Z","etag":null,"topics":["genomics","vcf"],"latest_commit_sha":null,"homepage":"","language":"Rust","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/brentp.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,"governance":null,"roadmap":null,"authors":null,"dei":null,"publiccode":null,"codemeta":null}},"created_at":"2023-09-11T13:01:27.000Z","updated_at":"2024-12-09T18:08:28.000Z","dependencies_parsed_at":"2023-09-11T14:58:48.420Z","dependency_job_id":"a6d6f1b3-bd4a-44f1-be7f-5ab7caab1dbb","html_url":"https://github.com/brentp/xvcf-rs","commit_stats":null,"previous_names":["brentp/xvcf-rs"],"tags_count":2,"template":false,"template_full_name":null,"repository_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brentp%2Fxvcf-rs","tags_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brentp%2Fxvcf-rs/tags","releases_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brentp%2Fxvcf-rs/releases","manifests_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/repositories/brentp%2Fxvcf-rs/manifests","owner_url":"https://repos.ecosyste.ms/api/v1/hosts/GitHub/owners/brentp","download_url":"https://codeload.github.com/brentp/xvcf-rs/tar.gz/refs/heads/main","host":{"name":"GitHub","url":"https://github.com","kind":"github","repositories_count":238882472,"owners_count":19546523,"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":["genomics","vcf"],"created_at":"2024-10-12T02:20:46.827Z","updated_at":"2025-10-29T19:31:42.304Z","avatar_url":"https://github.com/brentp.png","language":"Rust","funding_links":[],"categories":[],"sub_categories":[],"readme":"[![Continuous integration](https://github.com/brentp/xvcf-rs/actions/workflows/main.yml/badge.svg)](https://github.com/brentp/xvcf-rs/actions/workflows/main.yml)\n\nThis is a small library that attempts to allow efficient reading\nof VCF and BCF files that are either compressed or uncompressed and indexed or not.\n[rust_htslib](https://github.com/rust-bio/rust-htslib) is used for the parsing, this unifies handling above that.\n\nEven when not indexed, it allows \"skipping\" via iterating until the requested region is reached.\nThis is useful for [bedder-rs](https://github.com/quinlan-lab/bedder-rs) but might also be useful elsewhere.\n\nThe skipping will be most efficient when the files are compressed and indexed.\n\n\n## NOTES\n\nThis currently will may work as expected when there are multiple variants with the same position.\nThat will depend on how it is called. This will be fixed in the future.\n\n### Implementation\n\nAs implemented, only compressed, indexed VCF or BCF will have the absolute highest performance.\nOthers will require skipping via iterating over the file until the given region is reached.\nThis assumes that any indexed file will also support `Seek`.","project_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrentp%2Fxvcf-rs","html_url":"https://awesome.ecosyste.ms/projects/github.com%2Fbrentp%2Fxvcf-rs","lists_url":"https://awesome.ecosyste.ms/api/v1/projects/github.com%2Fbrentp%2Fxvcf-rs/lists"}