{"about":{"site":"https://codewithpapers.app","non_affiliation":"Code with Papers and Syntology are not affiliated with, endorsed by, or sponsored by Papers with Code, Meta, or the pwc-archive mirror.","licence":"CC BY-SA 4.0","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","attribution":"https://codewithpapers.app/attribution","modified":"archive material modified by Syntology; see the attribution page"},"url":"/paper/typesafe-coordinate-systems-in-high","title":"Typesafe Coordinate Systems in High-Throughput Sequencing Applications","arxiv_id":"2209.06603","date":"2022-09-14","proceeding":null,"authors":["Charles Thomas Gregory","James S. Blachly"],"abstract":"High-throughput sequencing file formats and tools encode coordinate intervals with respect to a reference sequence in at least four distinct, incompatible ways. Integrating data from and moving data between different formats has the potential to introduce subtle off-by-one errors. Here, we introduce the notion of typesafe coordinates: coordinate intervals are not only an integer pair, but members of a type class comprising four types: the Cartesian product of a zero or one basis, and an open or closed interval end. By leveraging the type system of statically and strongly-typed, compiled languages we can provide static guarantees that an entire class of error is eliminated. We provide a reference implementation in D as part of a larger work (dhtslib), and proofs of concept in Rust, OCaml, and Python. Exploratory implementations are available at https://github.com/blachlylab/typesafe-coordinates.","url_abs":"https://arxiv.org/abs/2209.06603v1","url_pdf":"https://arxiv.org/pdf/2209.06603v1.pdf","source":{"archive":"pwc-archive (Hugging Face), CC BY-SA 4.0","snapshot":"2025-07-28","licence_url":"https://creativecommons.org/licenses/by-sa/4.0/legalcode","row_kind":"abstracts"},"code_links":[{"paper_slug":"typesafe-coordinate-systems-in-high","repo_url":"https://github.com/blachlylab/typesafe-coordinates","is_official":1,"mentioned_in_paper":1,"mentioned_in_github":0,"framework":"none","reach":null}],"tasks":[{"task_slug":"high","task_name":"Vocal Bursts Intensity Prediction"}],"methods":[],"datasets_introduced":[],"methods_introduced":[],"results":[],"syntology":{"atlas_url":null,"mcp":null,"developers":"https://syntology.ai/developers"},"arxiv_metadata":null,"syntology_extracted_results":null}