odgi similarity

Provides a sparse similarity matrix for paths or groups of paths. Each line prints in a tab-delimited format to stdout.

SYNOPSIS

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

DESCRIPTION

The odgi similarity command allows the investigation of the similarity between (groups of) paths 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!

Path Investigation Options

-D, --delim=CHAR

The part of each path name before this delimiter is a group identifier.

-p, --delim-pos=N

Consider the N-th occurrence of the delimiter specified with -D, --delim to obtain the group identifier. Specify 1 for the 1st occurrence (default)."

-d, --distances

Provide distances (dissimilarities) instead of similarities. Outputs an additional column with the Euclidean distance.

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 paths.