Introduction

BioC++ is a project that encompasses multiple C++ libraries that each provide one or more modules. These modules cover typical tasks in Bioinformatics like storing sequence data or reading/writing file formats. The goal of BioC++ is to provide interfaces that are easier to use than those of the C and C++ libraries currently available while still delivering an excellent performance. It leverages Modern C++ to achieve this.

Module descriptions

Library	Module(s)	Description
Core	Alphabet	Datastructures for storing DNA, RNA and amino acids.
	Ranges	Containers and Views
	Meta	Metaprogramming utilities, concepts, tuples
I/O	I/O	Input/Output for TXT, CSV, FastA, FastQ, VCF, BCF, …

More modules are planned!

Repositories / CMake / Packages

Library	Github repo	CMake pkg	CMake lib
Core	biocpp/biocpp-core	biocpp_core	biocpp::core
I/O	biocpp/biocpp-io	biocpp_io	biocpp::io

CMake pkg: Include the library(s) with multiple calls to find_package(biocpp_core REQUIRED) (changing the respective CMake pkg) or with a single call to find_package(biocpp REQUIRED COMPONENTS core io [...]).

CMake lib: Add the respective library to your make target with target_link_libraries(your_target INTERFACE biocpp::core biocpp::io [...]).

Headers and namespaces

Library	Module(s)	Include	Namespaces	Code-Owner
Core	Alphabet	<bio/alphabet/*>	`bio::alphabet`	`@h-2`
	Ranges	<bio/ranges/*>	`bio::ranges`, `bio::{ranges::}views`	`@h-2`
	Meta	<bio/meta/*>	`bio::meta`	`@h-2`
I/O	I/O	<bio/io/*>	`bio::io`	`@h-2`

The primary namespace for BioC++ is bio::, and each Module is found in a sub-namespace (usually identical to the module name). Some namespaces are aliased into the primary namespace, so bio::ranges::views is identical to bio::views. Only top-level namespaces are displayed here.

Some modules provide literals in an inline namespace within their main namespace. This allows doing e.g. using namespace bio::alphabet::literals; to get easy access to the alphabet literals without importing the rest of the module into your namespace.

Attribution

If no citable publication is listed for a Module, please cite 10.1007/978-3-030-90990-1, which is a book by the main author of BioC++.