FastaVector

A simple C library for reading/writing fasta files. This library concatenates the headers of the fasta file into a buffer, concatenates the sequences into a separate buffer, and keeps a metadata buffer that allows for easy indexing into the fasta data to retrieve the headers/sequences via simple lookup table.

Building

This library uses CMake. To build the library, use:

cmake .
make

This will produce both static and dynamic versions of the library in the build/ directory. To install the dynamic version, use make install.

The necessary headers can be found in the src/ directory. The headers, along with the shared library can be installed using:

make install

Legacy Build

It is also possible to build using a handrolled Makefile, without CMake. To do this, use Makefile_legacy:

make -f Makefile_legacy

Tests

The library includes a suite of unit tests. They are found in the tests/ directory and can be run with make test after the build has been run (make).

The test binaries end up in the build/ directory with the rest of the output. You can run a suite on its own by running the corresponding binary from the correct test directory (since they use relative paths to access test fixtures). For example:

cmake .
make
cd tests/fileReadTest
../../build/fileReadTest

Formatting

Code is formatted automatically using clang-format version 12.0.0 or later. To run the formatter, using ./tool/run-format.sh. To check whether formatting is required, use ./tool/check-format.sh.

Note that formatting will occur automatically on pull requests, so manually running the formatter is unnecessary.

Using

For more info and the library API, please consult src/FastaVector.h and the test suite found in the tests/ directory.