vcfpp: a C++ API for rapid processing of the variant call format

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++ A...

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Veröffentlicht in:Bioinformatics (Oxford, England) Jg. 40; H. 2
1. Verfasser: Li, Zilong
Format: Journal Article
Sprache:Englisch
Veröffentlicht: England Oxford University Press 01.02.2024
Oxford Publishing Limited (England)
Schlagworte:
Application programming interface
Applications Note
Availability
C++ (programming language)
Format
ISSN:1367-4811, 1367-4803, 1367-4811
Online-Zugang:Volltext
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Zusammenfassung: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.
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ISSN:1367-4811
1367-4803
1367-4811
DOI:10.1093/bioinformatics/btae049