usage: hicHyperoptDetectLoopsHiCCUPS --matrix MATRIX --proteinFile PROTEINFILE
                                     MAXIMUMNUMBEROFLOOPS --juicerPath
                                     [--outputFileName OUTPUTFILENAME]
                                     [--resolution RESOLUTION] [--runs RUNS]
                                     [--threads THREADS] --normalization
                                     NORMALIZATION [--cpu] [--restricted]
                                     [--help] [--version]

Required arguments

--matrix, -m

The matrix to compute the loops on.

--proteinFile, -p

The protein file to validate the detected loops

--maximumNumberOfLoops, -ml

The maximum number of loops that should be used for optimization computation.

--juicerPath, -j

path to juicer.jar

--outputFileName, -o

File names for the result of the optimization (Default: “hyperoptHiCCUPS_result.txt”).

Default: “hyperoptHiCCUPS_result.txt”

Optional arguments

--resolution, -r

Resolution of matrix (Default: 10000).

Default: 10000


Number of runs of hyperopt.

Default: 100

--threads, -t

Number of threads (uses the python multiprocessing module) (Default: 4).

Default: 4

--normalization, -k

Normalization table name


use the CPU version

Default: False


If the GPU version is used, search only within 8 MB.

Default: False


show program’s version number and exit