Aligning genes to assembly graphs

Rationale

In theory, assembly graphs are much more complete than the contigs we end up writing to a FASTA file. So to check this we decided to do a small test with an A. thaliana w2rap-contigger assembly.

The idea is that if you look for both genes and or contiguous chunks of the genome in the assembly graph, as long as the appropriate connections exist, you can find the complete genes.

If we find this useful, we can probably include a little tool to do the alignments on the graph output of the w2rap-contigger and give you back a subset of the graph, and even stitch the paths together into an ad-hoc reference sequence chunk.

Looking for interesting (i.e. broken on