Closed anshumanmohan closed 1 year ago
I originally wanted to also do odgi inject
in the same PR, since it also has to do with fasta and bed.
In theory, running
odgi inject -i graph.og -b more_paths.bed -o graph_with_more_paths.og
produces a new graph, where any paths chalked out in more_paths.bed are inserted. The .bed file needs to be compatible with the given graph.
Sadly I'm not really able to run this as of writing. I made a k.bed
using k.og
, then simply changed the name of the path "x" into "z" (i.e., adding a new path that exactly coincides with the known-to-be-correct path "x") but found the resultant graph to be unchanged. I'll investigate further, including snooping around the codebase.
This PR adds support for
odgi flatten
. IMO it only really makes sense to run this command with both its flags supplied, though it is happy to run with either. Runningodgi flatten -i graph.og -f graph.fasta -b graph.bed
produces:It may be clear to see why these really go hand in hand: the former has no path information, and the latter has no sequence information.
It's a simple enough algorithm, and all tests pass with the current suite of graphs.