This project contains the source code and openCL/GPU bench for the phageterm project. I will leave it to the authors (Marc and Julian) to describe it and will just talk of the openCL benchmark part.
1. Mapping or reads
In the original version of phageterm, mapping reads than randomly choosing a mapping position for each read took approximatiely 80% of the execution time. It was done with the regexp python package. I studied several possibilities to reduce execution time.
* optimize regexp or use it differently
I first thought to that by I didn't find anything relevant except compiling the regexp element which is not of any use since it changes with each read.
* use another python package with special text searching algorithms.
