odgi extract¶
extract parts of the graph as defined by query criteria
SYNOPSIS¶
odgi extract [-f, –input-graphs=FILE] [-o, –out=FILE] [OPTION]…
DESCRIPTION¶
The odgi extract(1) command extracts parts of the graph as defined by query criteria.
OPTIONS¶
Graph Files IO¶
-f, –input-graphs=FILE
File containing the succinct variation graph. The file name usually
ends with .og.
-o, –out=FILE
Store all subgraph in this file. The file name usually ends with
.og.
Extract Options¶
-s, –split-subgraphs=STRING
Instead of writing the target subgraphs into a single graph, write one
subgraph per given target to a separate file named
path:start-end.og (0-based coordinates).-I, –inverse
Extract parts of the graph that do not meet the query criteria.
-l, –node-list::_FILE_
A file with one node id per line. The node specified will be extracted
from the input graph.
-n, –node::_STRING_
A single node from which to begin our traversal.
-c, –context::_NUMBER_
The number of steps away from our initial subgraph that we should
collect.
-L, –use-length
Treat the context size as a length in bases (and not as a number of
steps).
-r, –path-range
Find the node(s) in the specified path range TARGET=path[:pos1[-pos2]]
(0-based coordinates)
-r, –bed-file::_FILE_
Find the node(s) in the path range(s) specified in the given BED FILE
-E, –full-range
Collects all nodes in the sorted order of the graph in the min and max
position touched by the given path ranges. Be careful to use it with
very complex graphs.
-p, –paths-to-extract::_FILE_
List of paths to consider in the extraction; the file must contain one
path name per line and a subset of all paths can be specified.
-R, –lace-paths::_FILE_
List of paths to fully retain in the extracted graph; must contain one
path name per line and a subset of all paths can be specified.
Threading¶
-t, –threads=N
Number of threads to use (to embed the subpaths in parallel).
Processing Information¶
-P, –progress
Print information to stderr.
Program Information¶
-h, –help
Print a help message for odgi extract.