odgi build

construct a dynamic succinct variation graph

SYNOPSIS

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

DESCRIPTION

The odgi build(1) command constructs a succinct variation graph from a GFA. Currently, only GFA1 is supported. For details of the format please see https://github.com/GFA-spec/GFA-spec/blob/master/GFA1.md.

OPTIONS

Graph Files IO

-g, –gfa=FILE

GFA1 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.

Processing Information

-p, –progress

Print progress updates to stdout.

-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.

–trace

Include backtrace information when reporting errors.

-v, –verbose

Verbosely print processing information to stderr, including debug-level log messages.

-w, –warnings

Turn on script warnings (applies to executed code).

-t, –threads=N

Number of threads to use for the parallel operations.

Program Information

-h, –help

Print a help message for odgi build.