Introduction

IVio, pronounced for you aka io4. A c++20 library for bioinformatics. Providing functions for reading and writing different file formats.

Support

A list of currently supported file types:

	read support	write support
fasta	✔	✔
fasta+gzip	✔	✔
indexed fasta	✔	✘
fastq	✔	✘
fastq+gzip	✔	✘
vcf	✔	✔
bcf	✔	✘
sam	✔	✔
bam	✔	✘

Basic concepts

Each file type consist of different parts. Here we discuss it for the fasta format.

• fasta::reader
• fasta::writer
• fasta::record
• fasta::record_view

Integration CMake via CPM

Easiest way is using CPM by adding to your CMakeLists.txt

CPMAddPackage("gh:SGSSGene/iv-project/IVio@1.0.0")

#...
target_link_libraries(your_lib_or_exec PUBLIC ivio::ivio)

Thats it.

Integration CMake via subdirectory

Another way to use this repository is to clone this as a sub-repo into your project, for example to lib/IVio, and then edit your CMakeLists.txt:

find_package (ivio REQUIRED PATHS lib/IVio)

# ...
target_link_libraries(your_project ivio::ivio)

You can now happily use IVio

Example Code

Reading a fasta file:

#include <ivio/ivio.h>

int main() {
    auto reader = ivio::fasta::reader{{"somedata.fasta"}};
    for (auto record_view : reader) {
        std::cout << "id: " << record_view.id << "\n";
        std::cout << "seq: " << record_view.seq << "\n";
    }
}