vcfpp: a C++ API for rapid processing of the variant call format
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Motivation
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.
Results
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.
Availability and implementation
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.
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.
Results
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.
Availability and implementation
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.
Originalsprog | Engelsk |
---|---|
Artikelnummer | btae049 |
Tidsskrift | Bioinformatics |
Vol/bind | 40 |
Udgave nummer | 2 |
Antal sider | 4 |
ISSN | 1367-4803 |
DOI | |
Status | Udgivet - 2024 |
Bibliografisk note
Funding Information:
This work was supported by the Novo Nordisk 462 Foundation [NNF20OC0061343].
Publisher Copyright:
© 2024 Oxford University Press. All rights reserved.
ID: 389415862