ruanjue/bsalign

Banded Striped DNA Sequence Alignment

bsalign's Issues

how to compile in macOS x

I download the repo and run make in the directory, and an awful lot of error generated, any tips to successfully compile it in macOS ?

OpenMP parallel?

Hello Team,

It should be easy to just use openMP to parallel among the pairs to using multiple threads right since the library itself runs each pair sequentially. I see the thread.h but it is not used?

Thanks,

Jianshu

overlap mode and extend mode?

Dear BSAlign team,

I tried both mode, overlap mode is more like a semi-global mode that ignore gaps at both ends right, so only the overlap region that matters. However, for the extend mode, only gaps at the beginning of sequence 1 are extended while gaps at the end of it were not extended. I just trimmed the first sequence for 50 bp at both ends of it to do the testing. Any reasons for that?

Thanks,

Jianshu