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README.md

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C API

This directory contains an example of how to use the C API of block aligner.

Currently, only sequence to sequence and sequence to profile alignment with amino acid scoring matrices is supported with the C API. However, this can easily be adapted to align nucleotides by setting custom match/mismatch scores. Other features may be added if there is demand for them.

Running the example

  1. cd into this directory.
  2. Run make. This will build block aligner in release mode, use cbindgen to generate the header file, and make sure block aligner is linked to the example program. You only need to have cbindgen installed if you are making changes to the block aligner code and need to regenerate bindings. If you are only using the library, a generated header file is provided in this directory.
  3. Run ./a.out. This will run the example program to perform alignment calculations.

The generated header file, c/block_aligner.h, should be included in code that calls block aligner functions. It is C++ compatible. Like in the example Makefile, the block_aligner_c library in c/target/release must be linked to any C/C++ code that calls block aligner functions.

Note that this directory has a minimal Cargo.toml that has no dependencies, so block aligner can be compiled offline.