A Rust implementation of the algorithm described in Superbubbles, Ultrabubbles and Cacti paper.
Supports transforming a GFA graph into a biedged graph, and further into cactus graphs, cactus trees, and bridge forests.
These structures can then be used to find the ultrabubbles in the graph (see the paper for more details).
This crate can be used either as a command line application, or as a library in other Rust projects.
```bash $ saboten --help saboten 0.0.1
USAGE:
saboten [FLAGS]
FLAGS: -h, --help Prints help information -j, --json Output JSON -V, --version Prints version information
ARGS:
All the command line tool needs is the path to the input GFA.
The default output is one ultrabubble per line, with a tab between the start and end of the bubble, for example:
7 9
3 11
12 15
0 3
If the --json flag is turned on, output will instead be a JSON
array, where each element is an object with a start and an end
field, denoting the ultrabubble start and end nodes:
json
[{"start":7,"end":9},
{"start":3,"end":11},
{"start":12,"end":15},
{"start":0,"end":3}]
Library usage will look very much like the main() function of the
command line tool, transforming a GFA into a biedged graph, and then
building the rest of the graph structures off of that, before using
the cactus tree and bridge forest with the find_ultrabubbles_par
function.
Input graphs must have all segment names as unsigned integers, and tightly packed, e.g. from 0 to N-1, if there are N segments, however the numbering does not have to start from zero.