A parallel implementation of the haplotype assembly problem
Provides a parallel implementation of the haplotype assembly problem, that works with a multiple parallel hardware:
- GPU: This is the intended usage and provides the best performance, it uses CUDA.
- CPU: Parallel CPU implementation using Intel TBB.
- PHI: Intel Xeon Phi implementation, it uses Intel TBB
#Organisation
The repository is structured as follows:
|--- parahaplo
| |--- LICENCE.md
| |--- README.md
| |--- doc/ (documentation)
| | |--- prelim/ (preliminary report)
| | |--- final/ (final report)
| |--- haplo/ (source code)
| |--- ref/ (reference material)
| | |--- links.md (links to any relevant information)
| |--- tests/ (unit tests for library)
| | |--- block_tests.cpp (block tests)
| | |--- equality_checker_tests.cpp (tests for checking if rows/cols are equal)
| | |--- Makefile (Makefile for tests)
| | |--- small_container_tests.cpp (tests for small (binary) containers)
| | |--- tests.cpp (main test file for running all tests)
| | |--- unsplittable_block_tests.cpp (tests for unsplittable blocks)
| | |--- input_files/ (input files for tests)