odgi overlap

Find the paths touched by given input paths.


odgi overlap [-i, --input=FILE] [OPTION]…


The odgi overlap command finds the paths touched by the input paths.



-i, --input=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!

Overlap Options

-s, --subset-paths=FILE
Perform the search considering only the paths specified in the FILE; the file must contain one path name per line and a subset of all paths can be specified. When searching the overlaps, only these paths will be considered.
-r, --path=STRING
Perform the search of the given path STRING in the graph.
-R, --paths=FILE
Report the search results only for the paths listed in FILE.
-b, --bed-input=FILE
A BED file of ranges in paths in the graph.


-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 overlap.