A C++ version used in benchmarking https://github.com/liu-bioinfo-lab/scHiCTools.git mainly to compare the running time of reproducibility process.
Required C++ Package
- C++11
- Eigen
- MKL
- OpenMP
To reproduce the table of Magano 1000 cells: Linux cmd: Go to cmake loaction: cd scHiCEigen/cmake-build-debug/ Source mkl location to configure if needed: for example source /opt/intel/mkl/2021.1/setvars.sh
cmake -D CMAKE_CXX_COMPILER=/opt/gcc/8.4/modbin/g++ CMAKE_BUILD_TYPE=Release .. make ./scHiCEigen
Output will be in scHiCTest/cmake-build-debug/ files named $#ofcell$out.txt as well as print out
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