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 ...] [--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
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