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 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

MANDATORY OPTIONS

-i, --idx=FILE

Load the succinct variation graph index in xp format from this FILE. The file name usually ends with .xp.

-p, --path=STRING

The path name of the query.

-n, --nuc-pos=STRING

The nucleotide query of the query.

Program Information

-h, --help

Print a help message for odgi panpos.