odgi panpos

get the pangenome position of a given path and nucleotide position (1-based)

SYNOPSIS

odgi panpos [-i, –idx=FILE] [-p, –path=STRING] [-n, –nuc-pos=N] [OPTION]…

DESCRIPTION

The odgi panpos(1) command give a pangenome position for a given path and nucleotide position. It requires a path index, which can be created with odgi pathindex. Going from path:position → pangenome:position is important when navigating large graphs in an interactive manner like in the Pantograph project. All input and output positions are 1-based.

OPTIONS

Graph Files IO

-i, –idx=FILE

File containing the succinct variation graph index to find the pangenome position in. The file name usually ends with .xp.

Position Options

-p, –path=STRING

The path name of the query.

-n, –nuc-pos=STRING

The nucleotide sequence of the query.

Program Information

-h, –help

Print a help message for odgi panpos.