Yan Gao
Yan Gao
@glennhickey Can you share the dataset that causes the error/failure?
@glennhickey I did not get any error on my computer for this data. However, I did notice a big difference when using the scoring parameter you mentioned. Not only causes...
Thanks for the information! I am working on changing the scoring parameter options. Yan
> but only if abpoa can find enough seeds. If the sequences are too diverged, the memory can still explode. You are right, for divergent sequences, specifically with greatly different...
Hey @glennhickey , I am working on adding some interfaces related to memory usage by abPOA. Here is what I have done for now: Added 2 variables in abpoa_t: `status/req_mem`....
I have thought about using the size limit. The concern is that the size abpoc allocates is the virtual size, not the resident size, and the virtual size could be...
I don't fully get your idea. Do all the aligned sequences have flanking nucleotides? Or only a part of the sequences have? Then, I guess what you want is to...
``` >Multiple_sequence_alignment ------GGGGAAAAAAAATTTTGGGG TTTTTTGG--------TTTTTTGGGG TTTTTTGGGGAAAAAAAATTTTGGGG ``` I guess, from this new graph, what you want is the consensus of the original (unexpanded) sequences, right? Then the graph should be transformed...
See above, is that what you want?
Yes, theoretically, abPOA could take any type of seeding and chaining result to guide the POA process. I choose the minimizer simply out of speed consideration. Using a more mature...