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rapi

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.

Compiling

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.

Running tests

Run make tests

Using it

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).

Authors

RAPI is written by Luca Pireddu (pireddu@crs4.it).

Thanks go to these people for their contributions:

FAQ

Is the API stable?

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.