Fiuncho

     

What is Fiuncho?

Fiuncho is an epistasis detection program, implementing an exhaustive search of epistasis interactions of any given size. Fiuncho uses a SPMD (Single Program, Multiple Data) approach to accelerate the computation, exploiting the multiple cores available to a processor, or the multiple processors available in a cluster environment. Furthermore, Fiuncho takes advantage of the SIMD (Single Instruction, Multiple Data) vector operations available to each CPU core, offering multiple AVX implementations to support a wide variety of x86_64 processors.

Contents of this manual

• Installation
  • Downloading the source files
  • Configuring and building the CMake project
    • Advanced configuration
• Usage
  • Command-line usage
    • Named arguments
    • Positional arguments
    • Example
  • Data format
    • Input
    • Output
• Technical documentation
  • Using Fiuncho as a library
  • Classes documentation
    • Dataset class
    • GenotypeTable class
    • ContingencyTable class
    • MutualInformation class
    • Distribution class
    • MPIEngine class
    • Search class
    • ThreadedSearch class
• Licenses
  • GNU GPLv3
    • Preamble
    • Terms and conditions
    • How to apply these terms to your new programs
  • Third party software notices
    • sse-popcount

Reporting problems

If you find any problem using Fiuncho, an error in the documentation or something that can be improved, please open an Issue on Github describing the problem.