odgi validate

Validate a graph checking if the paths are consistent with the graph topology, and optionally with their source sequences.

SYNOPSIS

odgi validate [-i, --input=FILE] [-r, --fasta=FILE] [OPTION]…

DESCRIPTION

The odgi validate command checks that every pair of consecutive path steps is connected by an edge in the graph.

With -r, --fasta it also checks that each path spells out its source sequence, reporting counts of identical, divergent, missing path and missing source.

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 or GFAz (compressed GFA), but the on-the-fly conversion to the ODGI format requires additional time!

Sequence Validation

-r, --fasta=FILE

Check that every path spells out its source sequence in this uncompressed FASTA FILE. Records pair to paths by exact name, taken up to the first whitespace. The comparison is case-insensitive but symbol-exact, so N does not match A. The first difference is reported with its source position.

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 validate.