Yan Gao
Yan Gao
PAF format is nice. To feed abPOA, we only need to record which anchor comes from which sequence in the PAF file. Across multiple sequences may be too stringent, could...
The nodes in abPOA graph are all 1-base nodes. For your case, you can choose to add every single base one by one, this is also how abPOA creates the...
Thanks so much for writing the Rust repo for abPOA! Great work! I am still a new learner of Rust, but I think this is really nice and will make...
If all your sequences need to be aligned with abPOA, you can simply feed them to abpoa_msa, so that it will handle all the sequences. The very first sequence can...
If you have a graph that needs to be transformed to an abPOA graph, you have to add each node one by one, following a specific order, say DFS or...
> * convert each node of the variation graph into multiple abpoa nodes (in my code the "nodes" were `seq` and `seq2`) Then you can try it this way: >...
Thank you @ekg for providing this example. This is a bug related to the banding. So disable banded DP (set b as -1) is the easiest way to get rid...
@rvolden As mentioned by Erik, this new flag is not added in pyabpoa right now, I will get it done sone. However, I didn't implement the ambiguous strand mode in...
Anyway, the ultimate goal is to fix this bug instead of just break the loop and not provide any alignment result. I am working on that.
I modified the codes of the traceback part in the latest commit. Hopefully, this can resolve these bugs. I also removed the trackback_ok flag, since it is not needed if...