Added the ability for SegAlign to read and use a lastz scoring file.

[richard-burhans]

Added the ability for SegAlign to read and use a lastz scoring file. Before it would pass the scoring file to lastz, but it would not use the substitution scores itself. Instead it would use a matrix filled with zeroes. I added code from lastz to parse a scoring file and then copy it to the appropriate SegAlign structure. Details are below:

CMakeLists.txt updated CUDA_STANDARD from 11 to 14 added code to populate CMAKE_CUDA_ARCHITECTURES added code to parse a scoring file minor cleanup

scripts/get-cuda-arches.bash added code to populate CMAKE_CUDA_ARCHITECTURES

common/dna_utilities.c (from lastz source) common/dna_utilities.h (from lastz source) common/utilities.c (from lastz source) common/utilities.h (from lastz source) common/scoring.c common/scoring.h added code to parse a lastz scoring file

common/seed_pos_table.c added #include <thrust/execution_policy.h>

repeat_masker_src/seed_filter.cu src/seed_filter.cu added #include <thrust/sort.h>