odgi groom

Resolve spurious inverting links.

SYNOPSIS

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

DESCRIPTION

The odgi groom command resolves spurious inverting links.

OPTIONS

MANDATORY OPTIONS

-i, --idx=FILE

Load the succinct variation graph in ODGI format from this FILE. The file name usually ends with .og.

-o, --out=FILE

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

Grooming Options

-d, --use-dfs

Use depth-first search for the grooming.

-R, --target_paths=FILE

Read the paths that should be considered as target paths (references) from this FILE. odgi groom tries to force a forward orientation of all steps for the given paths. A path's rank determines it's weight for decision making and is given by its position in the given FILE.

Threading

-t, --threads=N

Number of threads to use for parallel operations.

Processing Information

-P, --progress

Write the current progress to stderr.

Program Information

-h, --help

Print a help message for odgi groom.