odgi overlap

Find the paths touched by given input paths.

SYNOPSIS

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

DESCRIPTION

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

OPTIONS

MANDATORY OPTIONS

-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.

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 overlap.