odgi pathindex

create a path index for a given path

SYNOPSIS

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

DESCRIPTION

The odgi pathindex(1) 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

Graph Files IO

-i, –idx=FILE

File containing the succinct variation graph to generate a path index from. The file name usually ends with .og.

-o, –out=FILE

Write the path index to FILE.

Program Information

-h, –help

Print a help message for odgi pathindex.