Enhancing performance - abyzovlab/CNVnator GitHub Wiki

The most time consuming step is partitioning of read-depth signal with mean-shift technique. There are few ways to make calculations at this step much faster.

1. Using Yepp library for fast calculation of exp() function

Yeppp is a library which provides high-performance implementations of math functions. To install with Yeppp support, download distribution package from here and extract it at a location of your choice. Set YEPPPLIBDIR and YEPPPINCLUDEDIR directories appropriately. Typically, for Linux-based systems on x86-64, YEPPPLIBDIR would be yeppp-1.0.0/binaries/linux/x86_64/ and YEPPPINCLUDEDIR would be yeppp-1.0.0/library/headers. Compile CNVnator with the command

        make YEPPPLIBDIR=<path_to_yepplibdir> YEPPPINCLUDEDIR=<path_to_yeppincludedir>

2. Using parallel implementation of partitioning with OpenMP

The work is in progress and updates software version will be available soon.