usage: hicHyperoptDetectLoopsHiCCUPS --matrix MATRIX --proteinFile PROTEINFILE
                                     MAXIMUMNUMBEROFLOOPS --juicerPath
                                     [--outputFileName OUTPUTFILENAME]
                                     [--resolution RESOLUTION]
                                     [--chrPrefixLoops {None,add,remove}]
                                     [--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

--chrPrefixLoops, -cl

Possible choices: None, add, remove

Adding / removing / do nothing a ‘chr’-prefix to chromosome name of the loops.


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