pyOpenCL module update

Some methods are no longer available/work differently in latest release of pyOpenCl. These are now fixed and still backwards-compatible.

OpenCL Improvements

Optimizations performed by @StreamHPC (@ex-rzr)

Docker + performance

Added docker containers and extensive performance tests

Affine Gap

This release contains the affine gap penalty scoring method. Previously released version 3.0 code for combar has been removed. ComBaR has now its own git page.

ComBaR, GenomePlotter release

This version contains the ComBar and GenomePlotter functionalities

OpenCL / CUDA update

Some bug fixes and feature enhancements

OpenCL release

This version contains the OpenCL Implementation by Roshan Timal of PaSWAS.

ComBaR release

The ComBaR functionality release

First stable release

This version of pyPaSWAS contains version 1.0 of the PaSWAS CUDA code. It supports:

• text output
• SAM output
• Programs: aligner, trimmer, indexer and mapper