odgi paths

Interrogate the embedded paths of a graph. Does not print anything to stdout by default!


odgi paths [-i, --idx=FILE] [OPTION]…


The odgi paths command allows the investigation of paths of a given variation graph. It can calculate overlap statistics of groupings of paths.



-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!

Path Investigation Options

-O, --overlaps=FILE
Read in the path grouping FILE to generate the overlap statistics from. The file must be tab-delimited. The first column lists a grouping and the second the path itself. Each line has one path entry. For each group the pairwise overlap statistics for each pairing will be calculated and printed to stdout.
-L, --list-paths
Print the paths in the graph to stdout. Each path is printed in its own line.
-l, --list-paths-start-end
If -L,--list-paths was specified, this additionally prints the start and end positions of each path in additional, tab-delimited coloumns.
-f, --fasta
Print paths in FASTA format to stdout. One line for the FASTA header, another line for the whole sequence.
-H, --haplotypes
Print to stdout the paths in an approximate binary haplotype matrix based on the graph’s sort order. The output is tab-delimited: path.name, path.length, path.step.count, node.1, node.2, node.n. Each path entry is printed in its own line.
-N, --scale-by-node-len
Scale the haplotype matrix cells by node length.
-D, --delim=CHAR
The part of each path name before this delimiter is a group identifier. For use with -H, --haplotypes: it prints an additional, first column group.name to stdout.
-p, --delim-pos=N
Consider the N-th occurrence of the delimiter specified with -D, --delim to obtain the group identifier. Specify 1 for the 1st occurrence (default)."

Path Modification Options

-K, --keep-paths=[FILE]
Keep paths listed (by line) in FILE.
-X, --drop-paths=[FILE]
Drop paths listed (by line) in FILE.
-o, --out=FILE
Write the dynamic succinct variation graph to this file (e.g. .og)


-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 paths.