odgi position¶
position parts of the graph as defined by query criteria
SYNOPSIS¶
odgi position [-i, –target=FILE] [OPTION]…
DESCRIPTION¶
The odgi position(1) command translates positions and coordinate ranges
between nodes and embedded paths. It provides liftover functionality,
allowing us to translate a position between any reference paths embedded
in the -i, --target graph. We can additionally project coordinates
and annotations from a source graph -x, --source into the
target. When completing this “graph lift”, the intersecting set of
paths in the two graphs are used to complete the coordinate projection.
OPTIONS¶
Graph Files IO¶
-i, –target=FILE
Describe positions in this graph.
-x, –source=FILE
Translate positions from this graph into the target graph using common
--lift-paths shared between both graphs [default: use the same
source/target graph]Position Options¶
-r, –ref-paths=STRING
Translate the given positions into positions relative to this
reference path.
-R, –ref-paths=FILE
Use the ref-paths in FILE.
-l, –lift-path=STRING
Lift positions from
--source to --target via coordinates in
this path common to both graphs [default: all common paths between
--source and --target].-g, –graph-pos=[[node_id][,offset[,(+|-)]**]**]
A graph position, e.g. 42,10,+ or 302,0,-.
-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 to lift into the target
graph
-v, --give-graph-pos emit graph positions.-v, –give-graph-pos
Emit graph positions (node,offset,strand) rather than path positions.
-I, –all-immediate
Emit all positions immediately at the given graph/path position.
-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 position.