WFA
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smarco
Wavefront alignment algorithm (WFA): Fast and exact gap-affine pairwise alignment
I am currently trying to use the `alignEndsFree` function in the WFA2 library to perform local alignment between pairs of sequences. However, I am having trouble obtaining the required input...
Is there a plan to implement Hamming distance calculation? It is probably trivial compared with other distance metrics, but really helps avoid using another library (so WFA2 all the way)...
Nice work! Would it be possible to get R bindings for this? I put together a minimal example here: https://github.com/traversc/WavefrontAlignR (feel free to do whatever with it) I'd also like...
We're getting into very nitpicky things now, but I noticed this, and who knows, maybe you can still fix it for some future version :smile: : - Equation 3 in...
Hi, there was a question by @brentp in issue #18 about how to retrieve the extent of an alignment: >> Also, is there an efficient way for this to get...
Hi, I'm using the code below to evaluate using wfa-lib to extend given a seed. Based on the docs, I though it would have to extend left and then right...
If you compile the latest https://github.com/armintoepfer/aligner-testbed with gcc10.3.0 with asan and ubsan ``` $ meson -Db_sanitize=address,undefined $ ninja $ ./at ../data/clr1.txt --rounds 1 --log-level INFO --miniwfa=false --ksw2=false | 20220421 10:31:22.817...
I'm running into an issue that I can't produce if I just give it one sequence pair... ``` wfa::WFAlignerGapAffine2Pieces aligner(4, 4, 2, 24, 1, wfa::WFAligner::Alignment, wfa::WFAligner::MemoryHigh); ``` ``` * thread...
When patching gaps between two anchors, we sometimes need to align two sequences of vastly different lengths. Suppose we are aligning a 10bp sequence against a 100kb sequence. The active...
Is it possible to set different score for insertion and deletion?
