odgi stats¶
metrics describing variation graphs
SYNOPSIS¶
odgi stats [-i, –idx=FILE] [OPTION]…
DESCRIPTION¶
The odgi stats(1) command produces statistics of a variation graph. Among other metrics, it can calculate the #nodes, #edges, #paths and the total nucleotide length of the graph. Various histogram summary options complement the tool. If [-B, –bed-multicov=BED] is set, the metrics will be produced for the intervals specified in the BED.
OPTIONS¶
Graph Files IO¶
-i, –idx=FILE
File containing the succinct variation graph to create statistics
from. The file name usually ends with .og.
Summary Options¶
-S, –summarize
Summarize the graph properties and dimensions. Print to stdout the
#nucleotides, #nodes, #edges and #paths of the graph.
-W, –weak-connected-components
Shows the properties of the weakly connected components.
-L, –self-loops
Number of nodes with a self-loop.
-N, –nondeterministic-edges
Show nondeterministic edges (those that extend to the same next base).
-b, –base-content
Describe the base content of the graph. Print to stdout the #A, #C, #G
and #T of the graph.
Sorting goodness evaluation¶
-l, –mean-links-length
Calculate the mean links length. This metric is path-guided and
computable in 1D and 2D.
-g, –no-gap-links
Don’t penalize gap links in the mean links length. A gap link is a
link which connects two nodes that are consecutive in the linear
pangenomic order. This option is specifiable only to compute the mean
links length in 1D.
-s, –sum-path-nodes-distances
Calculate the sum of path nodes distances. This metric is path-guided
and computable in 1D and 2D. For each path, it iterates from node to
node, summing their distances, and normalizing by the path length. In
1D, if a link goes back in the linearized viewpoint of the graph, this
is penalized (adding 3 times its length in the sum).
-d, –penalize-different-orientation
If a link connects two nodes which have different orientations, this
is penalized (adding 2 times its length in the sum).
-c, –coords-in
File containing the layout coordinates of the succinct variation graph
specified as input. The file name usually ends with .lay. When the
layout coordinates are provided, the mean links length and the sum
path nodes distances statistics are evaluated in 2D, else in 1D.
-P, –path-statistics
Display the statistics (mean links length or sum path nodes distances)
for each path.
Threading¶
-t, –threads=N
Number of threads to use.
Program Information¶
-h, –help
Print a help message for odgi stats.