odgi cover

Cover the graph with paths.

SYNOPSIS

odgi cover [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…

DESCRIPTION

The odgi cover command creates a path coverage of a variation graph, with a specified number of paths per component.

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!

-o, --out=FILE

Write the succinct variation graph with the generated paths in ODGI format to FILE. A file ending with .og is recommended.

Cover Options

-H, --hogwild-depth=DEPTH

Randomly cover the graph until it reaches the given average DEPTH. Specifying this options ignores all other Cover Options except -I, --ignore-paths!

-n, --num-paths-per-component=N

Number of paths to generate per component.

-k, --node-windows-size=N

Size of the node window to check each time a new path is extended (it has to be greater than or equal to 2).

-c, --min-node-coverage=N

Minimum node coverage to reach (it has to be greater than 0). There will be generated paths until the specified minimum node coverage is reached, or until the maximum number of allowed generated paths is reached (number of nodes in the input variation graph).

-I, --ignore-paths

Ignore the paths already embedded in the graph during the nodes coverage initialization.

-w, --write-node-coverages=FILE

Write the node coverages at the end of the paths generation to FILE. The file will contain tab-separated values (header included), and have 3 columns: component_id, node_id, and coverage.

Threading

-t, --threads=N

Number of threads to use for parallel operations.

Processing Information

-P, --progress

Print information about the components and the progress to stderr.

Program Information

-h, --help

Print a help message for odgi cover.