odgi pathindex

Create a path index for a given graph.

SYNOPSIS

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

DESCRIPTION

The odgi pathindex command generates a path index of a graph. It uses succinct data structures to encode the index. The path index represents a subset of the features of a fully realized xg index. Having a path index, we can use odgi panpos to go from path:position → pangenome:position which is important when navigating large graphs in an interactive manner like in the Pantograph project.

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 succinct variation graph index to this FILE. A file ending with .xp is recommended.

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 pathindex.