Section for Computational and RNA Biology, University of Copenhagen, Copenhagen 2200, Denmark.
Bioinformatics. 2024 Feb 1;40(2). doi: 10.1093/bioinformatics/btae049.
Given the widespread use of the variant call format (VCF/BCF) coupled with continuous surge in big data, there remains a perpetual demand for fast and flexible methods to manipulate these comprehensive formats across various programming languages.
This work presents vcfpp, a C++ API of HTSlib in a single file, providing an intuitive interface to manipulate VCF/BCF files rapidly and safely, in addition to being portable. Moreover, this work introduces the vcfppR package to demonstrate the development of a high-performance R package with vcfpp, allowing for rapid and straightforward variants analyses.
vcfpp is available from https://github.com/Zilong-Li/vcfpp under MIT license. vcfppR is available from https://cran.r-project.org/web/packages/vcfppR.
鉴于变体调用格式 (VCF/BCF) 的广泛使用以及大数据的持续激增，人们一直需要快速灵活的方法来跨各种编程语言处理这些综合格式。
这项工作提出了 vcfpp，它是 HTSlib 的一个 C++ API，包含在单个文件中，提供了一个直观的接口，可以快速、安全地处理 VCF/BCF 文件，并且可移植。此外，这项工作还引入了 vcfppR 包，以展示如何使用 vcfpp 开发高性能的 R 包，从而实现快速、直接的变体分析。
vcfpp 可从 https://github.com/Zilong-Li/vcfpp 获得，遵循 MIT 许可证。vcfppR 可从 https://cran.r-project.org/web/packages/vcfppR 获得。
