odgi depth¶
find the depth of graph as defined by query criteria
SYNOPSIS¶
odgi depth [-i, –input=FILE] [OPTION]…
DESCRIPTION¶
The odgi depth(1) command finds the depth of graph as defined by query criteria.
OPTIONS¶
Graph Files IO¶
-i, –input=FILE
Compute path depths in this graph.
Depth Options¶
-s, –subset-paths=FILE
Compute the depth 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.
-r, –path=STRING
Compute the depth of the given path in the graph.
-R, –paths=FILE
Compute depth for the paths listed in FILE.
-g, –graph-pos=[[node_id][,offset[,(+|-)]**]**]
Compute the depth at the given node, e.g. 7 or 3,4 or 42,10,+ or
302,0,-.
-G, –graph-pos-file=FILE
A file with graph path position per line.
-p, –path-pos=[[path_name][,offset[,(+|-)]**]**]
Return depth 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-depth
Compute the depth on each node in the graph.
-d, –search-radius=STRING
Limit coordinate conversion breadth-first search up to DISTANCE bp
from each given position [default: 10000].
Threading¶
-t, –threads=N
Number of threads to use.
Program Information¶
-h, –help
Print a help message for odgi depth.