odgi build

Construct a dynamic succinct variation graph in ODGI format from a GFAv1 or GFAz (compressed GFA)

SYNOPSIS

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

DESCRIPTION

The odgi build command constructs a succinct variation graph from a GFA. GFAv1 text and GFAz (a grammar-compressed GFA) are supported, and the input format is detected automatically by content. For details of the GFA format please see https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md.

OPTIONS

MANDATORY OPTIONS

-g, --gfa=FILE

GFAv1 or GFAz (compressed GFA) FILE containing the nodes, edges and paths to build a dynamic succinct variation graph from. GFAz input is detected automatically by content.

-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.

Threading

-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.