The BioC++ Core Library

This is the core library of the BioC++ project. It provides the following modules:

• Alphabet: data structures that represent single biological compounds like DNA, RNA and amino acids.
• Ranges: containers, views and utilities for storing and manipulating sequences of biological compounds.
• Meta: metaprogramming utilities and auxilliary data structures.

The design of this module is heavily influenced by C++ Ranges and C++ Concepts. An introduction into the topic can be found here.

General information on the BioC++ project can be found in the main repository. The full documention (all BioC++ modules) can found here.

Attention: this library is currently a work-in-progress. Getting it into a stable state is of highest priority, but until then all kinds of changes are still possible.

Example

std::vector seq = "GATTACATATA"_dna4;
auto translated = seq | bio::views::translate;

fmt::print("The six protein frames of '{}' are:\n{}\n", seq, translated);
/*
The six protein frames of 'GATTACATATA' are:
[DYI, ITY, LHI, YM*, ICN, YVI]
 */

fmt::print("The third frame's second amino acid is: {}\n", translated[2][1]);
/*
The third frame's second amino acid is: H
 */

Here translated appears like a vector of protein sequences, however, it is actually a "view", i.e. a light-weight, lazy-evaluated data structure. Its elements are computed on-the-fly and occupy no memory. It still supports constant-time random access like a vector.

Easy to use

• Header-only → just drop it in your source code or include it as a git submodule!
• Zero dependencies → keep complexity low!
• No build-system and no configure steps required.
• Optional CMake support available.
• Integrates well with the standard library, {fmt} and cereal.

State-of-the-art software engineering

• C++20 with good forward compatibility.
• GCC≥10 and Clang≥16 are supported.
• No warnings on -Wall -Wextra -pedantic.
• More than 97% code coverage.
• Automatic code-formatting with clang_format.
• Static analysis with clang_tidy.
• Runtime analysis with ASAN and UBSAN.
• No new or malloc in the entire codebase.

Quick-Setup

• Clone the repository: git clone https://github.com/biocpp/biocpp-core.git
• Add the include directory of BioC++, activate C++20 and you are good to go:

g++ -O3 -DNDEBUG -Wall -Wextra -std=c++20 -I /path/to/biocpp-core/include your_file.cpp

• If you want to use {fmt}, add -I /path/to/fmt/include -D FMT_HEADER_ONLY=1.