[cudaextender] Replace cudaextender's hardcoded encoding scheme with cudasequence

NVIDIA-Genomics-Research / GenomeWorks

SDK for GPU accelerated genome assembly and analysis

https://clara-parabricks.github.io/GenomeWorks/

Apache License 2.0

281 stars 76 forks source link

[cudaextender] Replace cudaextender's hardcoded encoding scheme with cudasequence #574

Open atadkase opened 3 years ago

atadkase commented 3 years ago

cudaextender/src/ungapped_xdrop.cu currently uses a hardcoded encoding scheme with fixed scoring matrices and a fixed alphabet. Replace that scheme with the generalized scheme that cudasequence will propose.