Bioio is a header-only, fast, C++11 library for FASTA/Q I/O. The API includes:

• Indexed fasta sequence reads.
• Non-indexed fasta record reading.
• Fastq record reading.

The library is intended to be as flexible as possible, including features such as:

• Templated methods, allowing any contiguous containers (e.g. std::vector and std::string) for sequences.
• Optional functional parameters which are applied to record names before extraction.

fasta.cpp is a simple command line application that uses bioio to fetch subsequences from an indexed fasta file. It can be compiled with make, and is used like

./fasta [options] <fasta_path> <region>

where options can include -i to set the index path, -s to output the length of the given sequence.

region is of the format contig:[begin]-[end] where begin and end are optional (e.g. X is all of contig X, and X:1000- is everything from 1000 to the end of X).

e.g.

./fasta human_g1k_v37.fasta X:1,000,000-1,000,100
./fasta human_g1k_v37.fasta 5:10,040,010-