odgi build

Construct a dynamic succinct variation graph in ODGI format from a GFAv1


odgi build [-g, --gfa=FILE] [-o, --out=FILE] [OPTION]…


The odgi build command constructs a succinct variation graph from a GFA. Currently, only GFAv1 is supported. For details of the format please see https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md.



-g, --gfa=FILE
GFAv1 FILE containing the nodes, edges and paths to build a dynamic succinct variation graph from.
-o, --out=FILE
Write the dynamic succinct variation graph to this FILE. A file ending with .og is recommended.

Graph Sorting

-s, --sort
Apply a general topological sort to the graph and order the node ids accordingly. A bidirected adaptation of Kahn’s topological sort (1962) is used, which can handle components with no heads or tails. Here, both heads and tails are taken into account.

Graph Optimization

-O, --optimize
Use the MutableHandleGraph::optimize method to compact the node identifier space.


-t, --threads=N
Number of threads to use for parallel operations.

Processing Information

-d, --debug
Verbosely print graph information to stderr. This includes the maximum node_id, the minimum node_id, the handle to node_id mapping, the deleted nodes and the path metadata.

Program Information

-h, --help
Print a help message for odgi build.
-P, --progress
Write the current progress to stderr.