Hajime Suzuki

Hi Ivan, I had a similar problem on my environment. The GraphMap (v0.3.1) segfaulted when aligning reads onto the D.melanogaster (dm6) genome. And here is my investigations: (line numbers are...

Hi Ivan, Thank you for your support and detailed fix report. I've confirmed that the updated graphmap properly processed the sequence that I had reported on my environments. Thank you...

Thank you all for fixing bugs, adding extremely useful features, and organizing the code for merging into this repository. I took a quick look at the code and there are...

I noticed now I had mistakenly commented to other place. As a record (and to keep it trackable) I add link and summary of the solution. * https://github.com/vgteam/vg/pull/1752#issuecomment-402259159 * The...

In my understanding ksw2 implements a similar formulation to the libgaba but is not dependent on it. Thankfully he refers my repository but ksw2 itself can be compiled and used...

Oh I didn't know that, thank you for your information. Then I'd like to inspect compatibility, or what version ksw2 expects for libgaba, so I'd be happy if you could...

Hi Dayana, First of all, the library does not support Windows environments (and also in the future). The library is developed for Linux and macOS so it would be the...

First of all, I'm sorry the bench.c being incorrect in calling the libgaba APIs. The correct one will be the following: ``` /* root coordinates; align from the heads */...

Sorry but, I personally don't recommend adopting adaptive banding for computing long alignments > 1kbp. It often lose track of optimal path when it enters a repetitive region, and breaks...

If banding matters in a sense of the quality of alignment, my personal conclusion is that the X-drop with anti-diagonal slicing is the best among existing algorithms. The threshold X...