eseiler/b.i.o.

The Biological Input-Output library

B.I.O. – the Biological Input/Output library

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.

Current state

The library is currently under heavy development. There is no release, yet, and all interfaces are subject to change.

Dependencies

	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

Usage

• 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).