odgi position
Find, translate, and liftover graph and path positions between graphs. Results are printed to stdout.
SYNOPSIS
odgi position [-i, --target=FILE] [OPTION]…
DESCRIPTION
The odgi position 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
MANDATORY OPTIONS
-i, --target=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!
Position Options
-x, --source=FILE
Translate positions from this FILE graph into the target graph using common
-l, --lift-paths shared between both graphs (default: use the same
source/target graph). It also accepts GFAv1, but the on-the-fly conversion to the ODGI format requires additional time!
-r, --ref-path=STRING
Translate the given positions into positions relative to this
reference path STRING.
-R, --ref-paths=FILE
Use the ref-paths in FILE for positional translation.
-l, --lift-path=STRING
Lift positions from -x, --source to -i, --target via coordinates in
this path common to both graphs (default: all common paths between
-x, --source and -i, --target).
-L, --lift-paths=FILE
Same as in -l, --lift-paths, but for all paths in FILE.
-g, --graph-pos=[[node_id][,offset[,(+|-)]**]**]
A graph position, e.g. 42,10,+ or 302,0,-.
-G, --graph-pos-file=FILE
Same as in -g, --graph-pos, but for all graph positions in FILE.
-p, --path-pos=[path_name][,offset[,(+|-)]]**
A path position, e.g. 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 to lift into the target
graph -v, --give-graph-pos emit graph positions.
-E, --gff-input=FILE
A GFF/GTF file with annotation of ranges in paths in the graph to lift into the target (sub)graph emitting graph identifiers with annotation. The output is a CSV reading for the visualization within Bandage. The first column is the node identifier, the second column the annotation. If several annotations exist for the same node, they are combined via ';'.
-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=DISTANCE
Limit coordinate conversion breadth-first search up to DISTANCE bp
from each given position (default: 10000).
-w, --jaccard-context=N
Maximum walking distance in nucleotides for one orientation when finding the best target (reference) range for each query path (default: 10000). Note: If we walked 9999 base pairs and w, --jaccard-context is 10000, we will also include the next node, even if we overflow the actual limit.
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 position.