using the protein alignment example in examples folder on pairs of proteins does not give correct results. The results were matched against the stripped smith-waterman library here (https://github.com/mengyao/complete-striped-smith-waterman-library). Debugging efforts revealed that scoring.substitute function does not return correct match/mismatch scores when called inside the kernel.
using the protein alignment example in examples folder on pairs of proteins does not give correct results. The results were matched against the stripped smith-waterman library here (https://github.com/mengyao/complete-striped-smith-waterman-library). Debugging efforts revealed that scoring.substitute function does not return correct match/mismatch scores when called inside the kernel.