Jeff Daily

I'm glad you got the build to work. This will help since you can evaluate my changes. I hope you have patience; this isn't going to be a quick/easy change.

I think I figured out how to produce what you want, but it does change the way semi-global is implemented internally. The original semi-global mode ("sg") would not penalize both...

@traversc I need your help with a new idea. I'm trying to preserve old behavior for maximum backwards compatibility, but I also see the value in your request. I'm thinking...

I'm having trouble understanding all the different approaches, as well. I don't have the cycles to spend a ton of time on this. Perhaps the name "stop local" is just...

What I meant about sgl producing negative numbers is that in the middle of the alignment algorithm the scores are allowed to be negative. Unlike with SW where scores are...

Looks like initially m4 is found already installed. `b'GNU M4 1.4.6'` But after automake is found to be missing, the build script installs all of the autotools (by design); m4,...

I'm assuming you were building from source since the parasail_aligner app isn't shipped as part of the wheel installs. - Is this Windows or Linux or MacOS? - Did you...

Also, if openmp was not found during configuration, you should receive a runtime warning if you specified -t but it wasn't supported. `-t number of threads requested, but OpenMP was...

The code is calling `omp_set_num_threads` and not doing anything else special. I found the following answer in stack overflow that might help you: https://stackoverflow.com/a/11096742. Try setting the env var OMP_DYNAMIC=0...

Is this still related to your original question of openmp not working? Can we open a new issue for the new observation `input file, query file, and stdin detected; max...