B.I.O. is a C++ library for reading and writing files in the field of Bioinformatics and in particular sequence analysis. It provides easy-to-use interfaces for the following formats:
- Plain I/O: plain-text, CSV, TSV, …
- Map I/O: SAM, BAM, …
- Seq I/O: FastA, FastQ, …
- Var I/O: VCF, BCF, …
The primary goal of this library is to offer higher level abstractions than the C libraries typically used in this domain (e.g. htslib) while at the same time offering an excellent performance. It hopes to offer a modern, well-integrated design that covers most typical I/O use-cases Bioinformaticians encounter.
The library relies strongly on Modern C++ and plays well with other Modern C++ libraries.
Please see the online documentation for more details.
The library is currently under heavy development. There is no release, yet, and all interfaces are subject to change.
| requirement | version | comment | |
|---|---|---|---|
| compiler | GCC | ≥ 10 | no other compiler is currently supported! |
| required libs | SeqAn3 | ≥ 3 | |
| optional libs | zlib | ≥ 1.2 | required for *.gz and .bam file support |
| bzip2 | ≥ 1.0 | required for *.bz2 file support |
- Using the library entails no build-steps, it is header-only and can be used as-is.
- A single-header version is available (TODO).
- CMake files are provided for easy integration into applications (and automatic detection/inclusion of dependencies).