odgi matrix

Write the graph topology in sparse matrix format.

SYNOPSIS

odgi matrix [-i, --idx=FILE] [OPTION]…

DESCRIPTION

The odgi matrix command generates a sparse matrix format out of the graph topology of a given variation graph.

OPTIONS

MANDATORY OPTIONS

-i, --idx=FILE

Load the succinct variation graph in ODGI format from this FILE. The file name usually ends with .og. It also accepts GFAv1, but the on-the-fly conversion to the ODGI format requires additional time!

Matrix Options

-e, --edge-depth-weight

Weigh edges by their path depth.

-d, --delta-weight

Weigh edges by their inverse id delta.

Threading

-t, --threads=N

Number of threads to use for parallel operations.

Processing Information

-P, --progress

Print information about the operations and the progress to stderr.

Program Information

-h, --help

Print a help message for odgi matrix.