odgi degree
Describe the graph in terms of node degree.
SYNOPSIS
odgi degree [-i, --idx=FILE] [OPTION]…
DESCRIPTION
The odgi degree command describes the graph in terms of node degree. In summarization mode, it shows the node.count, edge.count, avg.degree, min.degree, and max.degree. One can also specify degree ranges streaming these into a BED file.
OPTIONS
MANDATORY OPTIONS
-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!
Summary Options
-s, --subset-paths=FILE
Compute the degree considering only the paths specified in the FILE.
The file must contain one path name per line and a subset of all paths
can be specified. If a step is of a path of the given list, it is taken into account when calculating a node's depth. Else not.
-r, --path=STRING
Compute the degree of the given path STRING in the graph.
-R, --paths=FILE
Report the degree only for the paths listed in FILE.
-g, --graph-pos=[[node_id][,offset[,(+|-)]**]**]
Compute the degree at the given node, e.g. 7 or 3,4 or 42,10,+ or
302,0,-.
-G, --graph-pos-file=FILE
A file with one graph path position per line.
-p, --path-pos=[[path_name][,offset[,(+|-)]**]**]
Return degree at the given path position e.g. chrQ or chr3,42 or
chr8,1337,+ or chrZ,3929,-.
-F, --path-pos-file=FILE
A file with one path position per line.
-b, --bed-input=FILE
A BED file of ranges in paths in the graph.
-d, --graph-degree-table
Compute the degree and unique degree on each node in the graph, writing a table by node:
node.id, degree, and degree.uniq.
-v, --graph-degree-vec
Compute the degree on each node in the graph, writing a vector by base in one line.
-D, --path-degree
Compute a vector of degree on each base of each path. Each line consists of a path name
and subsequently the space-separated degree of each base.
-a, --self-degree
Compute the degree of the path versus itself on each base in each path. Each line consists of a path name
and subsequently the space-separated degree of each base.
-S, --summarize-graph-degree
Summarize the graph properties and dimensions. Print to stdout the
node.id and the node.degree.
-w, --windows-in=LEN:MIN:MAX
Print to stdout a BED file of path intervals where the degree is between MIN and MAX, merging the ranges not separated by more then LEN bp.
-W, --windows-out=LEN:MIN:MAX
Print to stdout a BED file of path intervals where the degree is outside MIN and MAX, merging the ranges not separated by more then LEN bp.
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 degree.