Prints information about a matrix or matrices including matrix size, number of elements, sum of elements, etc. An example usage is: $ hicInfo -m matrix1.h5 matrix2.h5 matrix3.h5

usage: hicInfo --matrices MATRICES [MATRICES ...] [--outFileName OUTFILENAME]
               [--no_metadata] [--help] [--version]

Required arguments

--matrices, -m

The matrix (or multiple matrices) to get information about. HiCExplorer supports the following file formats: h5 (native HiCExplorer format) and cool.

Optional arguments

--outFileName, -o

File name to save information of the matrix instead of writing it to the bash.

--no_metadata, -nm

Do not use meta data from cooler file to display information. This method is slower and was the default until version 2.2 of HiCExplorer. H5 files always use this parameter.

Default: True

--version, -v

show program’s version number and exit

An example output looks like this:

File:        hic_matrix.h5
WARNING: bin size is not homogeneous. Median 434
Size:        339,684
Sum: 243,779,407
Bin length:  434
Chromosomes: 2L, 2R, 3L, 3R, 4, X
Non-zero elements:   229,122,848
Minimum:     0
Maximum:     2116
NaN bins:    0

With HiCExplorer version 3 we support metadata in cooler files. The default behavior is to use the metadata:

$ hicInfo -m matrix.cool

To use the old method (and default for h5) please add the parameter:

$ hicInfo -m matrix.cool --no_metadata