Read aligner API
This project defines an API for a short read aligner (to map short reads to a reference sequence). It also includes a reference implementation that wraps BWA-MEM and Python bindings for the API.
Run make.
You'll need to have some tools on your system:
- git
- Swig 3
- python 2.x, including dev files
- python-setuptools
- zlib-dev
Plus everything necessary to build C programs.
Run make tests
That's too complicated to explain in this README file :-D
C interface +++++++++++++++
The API is defined in include/rapi.h. You can find an example showing how to
use it under example/rapi_test.c. The only plug-in implementation existing at
the moment wraps BWA-MEM; you can find it under rapi_bwa, where you'll also
find a static library (after building it, of course) that you can link to your
own programs.
Python interface +++++++++++++++++++
An equally interesting bit is the Python interface to RAPI, which you can
find under pyrapi. The script example/align.py implements a command-line
interface to the aligner (you can use it to align reads in fastq files and
generate SAM).
RAPI is written by Luca Pireddu (pireddu@crs4.it).
Thanks go to these people for their contributions:
- Riccardo Berutti (berutti@berutti.net)
- Sebastian Schoenherr (sebastian.schoenherr@uibk.ac.at)
No, it's not. The implementation works, but the API is still under development and thus will change. If you use it, do provide your suggestions on how to improve it.