├── .gitignore ├── LICENSE ├── Makefile ├── Readme.md ├── allqueries.fasta ├── benchmarksetup.sh ├── runpeakbenchmark.sh ├── runsprotbenchmark.sh ├── runtremblbenchmark.sh ├── rununiref50benchmark.sh └── src ├── blosum.cu ├── blosum.hpp ├── config.hpp ├── convert.cuh ├── cudasw4.cuh ├── dbbatching.cuh ├── dbdata.cpp ├── dbdata.hpp ├── dpx_s16_kernel_instantiations.cu ├── dpx_s16_kernels.cuh ├── dpx_s32_kernel_instantiations.cu ├── dpx_s32_kernels.cuh ├── float_kernel_instantiations.cu ├── float_kernels.cuh ├── gpudatabaseallocation.cuh ├── gridsearch.cu ├── half2_kernel_instantiations.cu ├── half2_kernels.cuh ├── hpc_helpers ├── all_helpers.cuh ├── coop_group_helpers.cuh ├── cuda_helpers.cuh ├── cuda_raiiwrappers.cuh ├── custom_thrust_allocators.cuh ├── hashers.cuh ├── hpc_helpers.h ├── io_helpers.h ├── nvtx_markers.cuh ├── packed_types.cuh ├── peer_access.cuh ├── simple_allocation.cuh ├── timers.cuh ├── type_helpers.h └── utility_kernels.cuh ├── kernelhelpers.cuh ├── kernels.cuh ├── kseqpp ├── filereader.hpp ├── gziphelpers.hpp └── kseqpp.hpp ├── length_partitions.hpp ├── main.cu ├── makedb.cpp ├── mapped_file.hpp ├── mmapbuffer.hpp ├── modifydb.cpp ├── oldkernels.cuh ├── options.cpp ├── options.hpp ├── sequence_io.cpp ├── sequence_io.h ├── types.hpp └── util.cuh /.gitignore: -------------------------------------------------------------------------------- 1 | align 2 | makedb 3 | modifydb 4 | build/ -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/asbschmidt/CUDASW4/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/asbschmidt/CUDASW4/HEAD/Makefile -------------------------------------------------------------------------------- /Readme.md: 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