This is an experimental odgi-like tool for manipulating pangenome graphs in the popular GFA format. It works by converting the GFA to a "flat," pointer-free representation that can be stored directly on disk for zero-copy reads and writes.
It's a Rust project, so all you need to do is:
$ cargo build --release
Then you might like to do something like this to put a symlink on your $PATH:
$ ln -s `pwd`/target/release/fgfa ~/.local/bin
Now see what's available:
$ fgfa --help
This tool can run queries directly on GFA text files, but you can amortize that cost by converting to the native FlatGFA format. Try this:
$ fgfa -I chr22.hprc-v1.0-pggb.gfa -o chr22.flatgfa
In general, you will want to remember these flags for input and output:
-ior-o: Read or write our native FlatGFA binary format.-Ior-O: Read or write the standard GFAv1 text format. Or, just omit the relevant flag to use standard input or standard output.
So combining -I and -o as above does the conversion you want. FlatGFA files should be a little smaller than their text counterparts. Now that we have one, we can convert it back to a GFA text file like this:
$ fgfa -i chr22.flatgfa | less
Here are some things we can do with FlatGFA files. See some basic statistics about the graph:
$ fgfa -i chr22.flatgfa stats -S
Or use -L instead to see information about self-loops. This output should match odgi stats.
Get a list of all the path names in the graph---or, in this case, just the first few:
$ fgfa -i chr22.flatgfa paths | head
Find the graph position of a given base-pair offset within a certain path, just like odgi position -v:
$ fgfa -i chr22.flatgfa position -p chm13#chr22,12345,+
Extract a subgraph from a larger graph around a specific segment:
$ fgfa -i chr22.flatgfa -o chr22.sub.flatgfa extract -n 25 -c
$ fgfa -i chr22.sub.flatgfa stats -S
Unfortunately, this extraction doesn't quite match odgi extract yet (because I haven't quite been able to figure out how it's supposed to work).