Closed dirkjanvw closed 1 month ago
Ok, so the problem is that W
line appear before L
. As we are doing stream parsing we build graph on-fly. Therefore at the time of W
record processing there are no edges between segments / nodes. I will fix, so the proper message / exception will be thrown.
We do not segfault after https://github.com/asl/BandageNG/commit/a6adcc353e50cb16b17bae477a06582c94818672
However, the producer of this GFA should be fixed. Per GFA spec – "A valid walk must exist in the graph". We treat this quite strict as otherwise we will need essentially to save the copy of entire GFA before processing.
Thank you for the quick fix! I now "sorted" the graph by putting all W-lines at the end of the file, I think that should solve the processing issue? However, it doesn't complete parsing. I let BandageNG info mc-pangenome.sorted.gfa
run for an hour before I killed the process. Were you able to parse this GFA file in reasonable time?
Can you attach the new file, so I can check?
Of course: mc-pangenome.sorted.gfa.gz I had to gzip the file, wheareas I ran BandageNG info
with the uncompressed version, assuming this has no effect.
Of course: mc-pangenome.sorted.gfa.gz I had to gzip the file, wheareas I ran
BandageNG info
with the uncompressed version, assuming this has no effect.
Sorry, somehow I forgot to respond. Looks like it was me reading GFA spec improperly. Need to push the fix
Should be fixed in 24907eb
Thanks a lot, it works for me now!
As mentioned in #149 I get a segmentation fault on branch
walks
, which I don't get on branchdev
with my Macbook Pro. Example GFA file I obtained from the Minigraph-Cactus pipeline can be found here: mc-pangenome.gfa.gz. Let me know if there is anything else I can provide to figure out why this happens.