hicInfo

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 ...] [--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), npz (format used by earlier versions of HiCExplorer), dekker (matrix format used in Job Dekker publications), and lieberman (format used by Erez Lieberman Aiden). This last formats may change in the future.

Optional arguments

–version

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