######### odgi groom #########
Resolve spurious inverting links.
odgi groom [-i, --idx=FILE] [-o, --out=FILE] [OPTION]…
The odgi groom command resolves spurious inverting links.
MANDATORY OPTIONS --------------
-i, --idx=FILE
Load the succinct variation graph in ODGI format from this FILE. The file name usually ends with .og.
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.
Write the groomed succinct variation graph in ODGI format to FILE. A file ending with .og is recommended.
-d, --use-dfs
Use depth-first search for the grooming.
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.
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.
-t, --threads=N
Number of threads to use for parallel operations.
Number of threads to use for parallel operations.
-P, --progress
Write the current progress to stderr.
Write the current progress to stderr.
-h, --help
Print a help message for odgi groom.
Print a help message for odgi groom.