odgi break

Break cycles in the graph and drop its paths.

SYNOPSIS

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

DESCRIPTION

The odgi break command finds cycles in a graph via breadth-first search (BFS) and breaks them, also dropping the graph’s paths.

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 broken graph in ODGI format to FILE. A file ending of .og is recommended.

Cycle Options

-c, --cycle-max-bp=N

The maximum cycle length at which to break (default: 0).

-s, --max-search-bp=N

The maximum search space of each BFS given in number of base pairs (default: 0).

-u, --repeat-up-to=N

Iterate cycle breaking up to N times or stop if no new edges are removed.

-d, --show

Print the edges we would remove to stdout.

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 break.