odgi paths¶
embedded path interrogation
SYNOPSIS¶
odgi paths [-i, –idx=FILE] [OPTION]…
DESCRIPTION¶
The odgi paths(1) command allows the investigation of paths of a given variation graph. It can calculate overlap statistics of groupings of paths.
OPTIONS¶
Graph Files IO¶
-i, –idx=FILE
File containing the succinct variation graph to investigate the paths
from. The file name usually ends with .og.
-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.
Investigation Options¶
-L, –list-paths
Print the paths in the graph to stdout. Each path is printed in its
own line.
-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, node.count, node.1,
node.2, node.n. Each path entry is printed in its own line.
-D, –delim=CHAR
The part of each path name before this delimiter is a group
identifier. This parameter should only be set in combination with
[-H, –haplotypes]. Prints an additional, first column
group.name to stdout.
-d, –distance
Provides a sparse distance matrix for paths. If [-D, –delim] is
set, it will be path groups distances.
-f, –fasta
Print paths in FASTA format to stdout.
Threading¶
-t, –threads=N
Number of threads to use.
Program Information¶
-h, –help
Print a help message for odgi paths.