├── .clang-format ├── .gitattributes ├── .gitmodules ├── CMakeLists.txt ├── LICENSE ├── README.md ├── VERSION ├── ci ├── checks │ ├── changelog.sh │ ├── check_copyright.py │ └── style.sh ├── common │ ├── build-test-sdk.sh │ ├── logger.sh │ ├── prep-init-env.sh │ ├── prep-pull-repo-mr-branch.sh │ └── test-pygenomeworks.sh ├── cpu │ ├── build.sh │ └── prebuild.sh ├── gpu │ ├── build.sh │ └── prebuild.sh ├── local │ ├── build.sh │ └── prebuild.sh └── release │ ├── pypi_uploader.sh │ └── update-version.sh ├── cmake ├── 3rdparty.cmake ├── Benchmarks.cmake ├── BuildHTSLib.cmake ├── CUDA.cmake ├── CXX.cmake ├── CondaEnv.cmake ├── Doxygen.cmake ├── Format.cmake ├── GitVersion.cmake ├── Packaging.cmake ├── Tests.cmake └── Utils.cmake ├── common ├── base │ ├── CMakeLists.txt │ ├── include │ │ └── claraparabricks │ │ │ └── genomeworks │ │ │ ├── gw_config.hpp │ │ │ ├── logging │ │ │ └── logging.hpp │ │ │ ├── types.hpp │ │ │ ├── utils │ │ │ ├── allocator.hpp │ │ │ ├── cudasort.cuh │ │ │ ├── cudautils.hpp │ │ │ ├── device_buffer.hpp │ │ │ ├── device_preallocated_allocator.cuh │ │ │ ├── exceptions.hpp │ │ │ ├── genomeutils.hpp │ │ │ ├── graph.hpp │ │ │ ├── limits.cuh │ │ │ ├── mathutils.hpp │ │ │ ├── pinned_host_vector.hpp │ │ │ ├── signed_integer_utils.hpp │ │ │ ├── stringutils.hpp │ │ │ └── threadsafe_containers.hpp │ │ │ └── version.hpp │ ├── src │ │ ├── cudautils.cpp │ │ ├── graph.cpp │ │ ├── logging.cpp │ │ └── version.cpp.in │ └── tests │ │ ├── CMakeLists.txt │ │ ├── TestGraph.cpp │ │ ├── Test_DevicePreallocatedAllocator.cu │ │ ├── Test_GenomeUtils.cpp │ │ ├── Test_UtilsCudasort.cu │ │ ├── Test_UtilsThreadsafeContainers.cpp │ │ └── main.cpp └── io │ ├── CMakeLists.txt │ ├── include │ └── claraparabricks │ │ └── genomeworks │ │ └── io │ │ └── fasta_parser.hpp │ └── src │ ├── fasta_parser.cpp │ ├── kseqpp_fasta_parser.cpp │ └── kseqpp_fasta_parser.hpp ├── cudaaligner ├── CMakeLists.txt ├── README.md ├── benchmarks │ ├── CMakeLists.txt │ ├── README.md │ └── main.cpp ├── include │ └── claraparabricks │ │ └── genomeworks │ │ └── cudaaligner │ │ ├── aligner.hpp │ │ ├── alignment.hpp │ │ └── cudaaligner.hpp ├── samples │ ├── CMakeLists.txt │ └── sample_cudaaligner.cpp ├── src │ ├── aligner.cpp │ ├── aligner_global.cpp │ ├── aligner_global.hpp │ ├── aligner_global_hirschberg_myers.cpp │ ├── aligner_global_hirschberg_myers.hpp │ ├── aligner_global_myers.cpp │ ├── aligner_global_myers.hpp │ ├── aligner_global_myers_banded.cpp │ ├── aligner_global_myers_banded.hpp │ ├── aligner_global_ukkonen.cpp │ ├── aligner_global_ukkonen.hpp │ ├── alignment.cpp │ ├── alignment_impl.cpp │ ├── alignment_impl.hpp │ ├── batched_device_matrices.cuh │ ├── cudaaligner.cpp │ ├── hirschberg_myers_gpu.cu │ ├── hirschberg_myers_gpu.cuh │ ├── matrix_cpu.hpp │ ├── myers_cpu.hpp │ ├── myers_gpu.cu │ ├── myers_gpu.cuh │ ├── needleman_wunsch_cpu.cpp │ ├── needleman_wunsch_cpu.hpp │ ├── ukkonen_cpu.cpp │ ├── ukkonen_cpu.hpp │ ├── ukkonen_gpu.cu │ └── ukkonen_gpu.cuh └── tests │ ├── CMakeLists.txt │ ├── Test_AlignerGlobal.cpp │ ├── Test_AlignmentImpl.cpp │ ├── Test_ApproximateBandedMyers.cpp │ ├── Test_HirschbergMyers.cu │ ├── Test_Misc.cpp │ ├── Test_MyersAlgorithm.cu │ ├── Test_NeedlemanWunschImplementation.cpp │ ├── cudaaligner_test_cases.cpp │ ├── cudaaligner_test_cases.hpp │ └── main.cpp ├── cudaextender ├── CMakeLists.txt ├── README.md ├── data │ ├── CMakeLists.txt │ ├── cudaextender_file_location.hpp.in │ ├── sample.fa │ ├── sample_scored_segment_pairs.csv │ └── sample_seed_pairs.csv ├── include │ └── claraparabricks │ │ └── genomeworks │ │ └── cudaextender │ │ ├── cudaextender.hpp │ │ ├── extender.hpp │ │ └── utils.hpp ├── samples │ ├── CMakeLists.txt │ └── sample_cudaextender.cpp ├── src │ ├── cudaextender.cpp │ ├── extender.cpp │ ├── ungapped_xdrop.cu │ ├── ungapped_xdrop.cuh │ ├── ungapped_xdrop_kernels.cu │ └── ungapped_xdrop_kernels.cuh └── tests │ ├── CMakeLists.txt │ ├── Test_CudaextenderEnd2End.cu │ └── main.cpp ├── cudamapper ├── CMakeLists.txt ├── README.md ├── data │ ├── 10_reads.fasta │ ├── 20_reads.fasta │ ├── CMakeLists.txt │ ├── aaaactgaa_gccaaag.fasta │ ├── aaaactgaa_gccaaag.fasta.fai │ ├── aagcta.fasta │ ├── catcaag.fasta │ ├── catcaag_aagcta.fasta │ ├── catcaag_aagcta.fasta.fai │ ├── cccatacc.fasta │ ├── cccatacc.fasta.fai │ ├── covid-reads.fasta.gz │ ├── cudamapper_file_location.hpp.in │ ├── gatt.fasta │ └── gatt.fasta.fai ├── include │ └── claraparabricks │ │ └── genomeworks │ │ └── cudamapper │ │ ├── cudamapper.hpp │ │ ├── index.hpp │ │ ├── matcher.hpp │ │ ├── overlapper.hpp │ │ ├── sketch_element.hpp │ │ ├── types.hpp │ │ └── utils.hpp ├── samples │ ├── CMakeLists.txt │ └── sample_cudamapper.cpp ├── src │ ├── application_parameters.cpp │ ├── application_parameters.hpp │ ├── cudamapper.cpp │ ├── cudamapper_utils.cpp │ ├── cudamapper_utils.hpp │ ├── index.cu │ ├── index_batcher.cu │ ├── index_batcher.cuh │ ├── index_cache.cu │ ├── index_cache.cuh │ ├── index_descriptor.cpp │ ├── index_gpu.cu │ ├── index_gpu.cuh │ ├── index_host_copy.cu │ ├── index_host_copy.cuh │ ├── main.cu │ ├── matcher.cu │ ├── matcher_gpu.cu │ ├── matcher_gpu.cuh │ ├── minimizer.cu │ ├── minimizer.hpp │ ├── overlapper.cpp │ ├── overlapper_triggered.cu │ ├── overlapper_triggered.hpp │ └── utils.cpp └── tests │ ├── CMakeLists.txt │ ├── Test_CudamapperIndexBatcher.cu │ ├── Test_CudamapperIndexCache.cu │ ├── Test_CudamapperIndexDescriptor.cpp │ ├── Test_CudamapperIndexGPU.cu │ ├── Test_CudamapperMatcherGPU.cu │ ├── Test_CudamapperMinimizer.cpp │ ├── Test_CudamapperOverlapper.cpp │ ├── Test_CudamapperOverlapperTriggered.cu │ ├── Test_CudamapperUtilsKmerFunctions.cpp │ ├── main.cpp │ ├── mock_fasta_parser.hpp │ └── mock_index.cuh ├── cudapoa ├── CMakeLists.txt ├── README.md ├── benchmarks │ ├── CMakeLists.txt │ ├── README.md │ ├── main.cpp │ ├── multi_batch.hpp │ └── single_batch.hpp ├── data │ ├── CMakeLists.txt │ ├── file_location.hpp.in │ ├── sample-bonito.txt │ ├── sample-golden-value.txt │ └── sample-windows.txt ├── include │ └── claraparabricks │ │ └── genomeworks │ │ └── cudapoa │ │ ├── batch.hpp │ │ ├── cudapoa.hpp │ │ └── utils.hpp ├── samples │ ├── CMakeLists.txt │ └── sample_cudapoa.cpp ├── src │ ├── allocate_block.hpp │ ├── application_parameters.cpp │ ├── application_parameters.hpp │ ├── batch.cu │ ├── cudapoa.cpp │ ├── cudapoa_add_alignment.cuh │ ├── cudapoa_batch.cuh │ ├── cudapoa_generate_consensus.cuh │ ├── cudapoa_generate_msa.cuh │ ├── cudapoa_kernels.cuh │ ├── cudapoa_limits.hpp │ ├── cudapoa_nw.cuh │ ├── cudapoa_nw_banded.cuh │ ├── cudapoa_nw_tb_banded.cuh │ ├── cudapoa_structs.cuh │ ├── cudapoa_topsort.cuh │ ├── main.cpp │ └── utils.cu └── tests │ ├── CMakeLists.txt │ ├── Test_CudapoaAddAlignment.cu │ ├── Test_CudapoaBatch.cu │ ├── Test_CudapoaBatchEnd2End.cu │ ├── Test_CudapoaGenerateConsensus.cu │ ├── Test_CudapoaGenerateMSA2.cu │ ├── Test_CudapoaNW.cu │ ├── Test_CudapoaSerializeGraph.cpp │ ├── Test_CudapoaTopSort.cu │ ├── basic_graph.hpp │ ├── main.cpp │ └── sorted_graph.hpp ├── docs └── Doxyfile.in └── pygenomeworks ├── .flake8.cython ├── README.md ├── bin ├── alignment_visualizer ├── evaluate_paf └── genome_simulator ├── generate_docs ├── genomeworks ├── __init__.py ├── cuda │ ├── __init__.py │ ├── cuda.pxd │ ├── cuda.pyx │ └── cuda_runtime_api.pxd ├── cudaaligner │ ├── __init__.py │ ├── cudaaligner.pxd │ └── cudaaligner.pyx ├── cudapoa │ ├── __init__.py │ ├── cudapoa.pxd │ ├── cudapoa.pyx │ └── graph.pxd ├── io │ ├── __init__.py │ ├── fastaio.py │ ├── pafio.py │ └── utils.py ├── simulators │ ├── __init__.py │ ├── genomesim.py │ └── readsim.py └── utilities │ ├── __init__.py │ └── utilities.py ├── python-style-requirements.txt ├── requirements.txt ├── samples ├── sample_cudaaligner └── sample_cudapoa ├── setup.cfg ├── setup.py ├── setup_pygenomeworks.py ├── style_check └── test ├── data ├── assembly_GT.fa ├── assembly_GT.gfa ├── overlaps_GT.paf ├── overlaps_on_assembly_GT.paf ├── polished_assembly_CPU_subgraph_GT.fa ├── reads.fasta └── ref.fasta ├── test_cuda_bindings.py ├── test_cudaaligner_bindings.py ├── test_cudapoa_bindings.py ├── test_genome_simulator.py ├── test_overlap_generator.py └── test_read_simulators.py /.clang-format: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/.clang-format -------------------------------------------------------------------------------- /.gitattributes: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/.gitattributes -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/.gitmodules -------------------------------------------------------------------------------- /CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/CMakeLists.txt -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/LICENSE -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/README.md -------------------------------------------------------------------------------- /VERSION: -------------------------------------------------------------------------------- 1 | 0.6.0 2 | 3 | -------------------------------------------------------------------------------- /ci/checks/changelog.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/checks/changelog.sh -------------------------------------------------------------------------------- /ci/checks/check_copyright.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/checks/check_copyright.py -------------------------------------------------------------------------------- /ci/checks/style.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/checks/style.sh -------------------------------------------------------------------------------- /ci/common/build-test-sdk.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/common/build-test-sdk.sh -------------------------------------------------------------------------------- /ci/common/logger.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/common/logger.sh -------------------------------------------------------------------------------- /ci/common/prep-init-env.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/common/prep-init-env.sh -------------------------------------------------------------------------------- /ci/common/prep-pull-repo-mr-branch.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/common/prep-pull-repo-mr-branch.sh -------------------------------------------------------------------------------- /ci/common/test-pygenomeworks.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/common/test-pygenomeworks.sh -------------------------------------------------------------------------------- /ci/cpu/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/cpu/build.sh -------------------------------------------------------------------------------- /ci/cpu/prebuild.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/cpu/prebuild.sh -------------------------------------------------------------------------------- /ci/gpu/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/gpu/build.sh -------------------------------------------------------------------------------- /ci/gpu/prebuild.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/gpu/prebuild.sh -------------------------------------------------------------------------------- /ci/local/build.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/local/build.sh -------------------------------------------------------------------------------- /ci/local/prebuild.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/local/prebuild.sh -------------------------------------------------------------------------------- /ci/release/pypi_uploader.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/release/pypi_uploader.sh -------------------------------------------------------------------------------- /ci/release/update-version.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/ci/release/update-version.sh -------------------------------------------------------------------------------- /cmake/3rdparty.cmake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cmake/3rdparty.cmake -------------------------------------------------------------------------------- /cmake/Benchmarks.cmake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cmake/Benchmarks.cmake -------------------------------------------------------------------------------- /cmake/BuildHTSLib.cmake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cmake/BuildHTSLib.cmake -------------------------------------------------------------------------------- /cmake/CUDA.cmake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cmake/CUDA.cmake -------------------------------------------------------------------------------- /cmake/CXX.cmake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cmake/CXX.cmake -------------------------------------------------------------------------------- /cmake/CondaEnv.cmake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cmake/CondaEnv.cmake -------------------------------------------------------------------------------- /cmake/Doxygen.cmake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cmake/Doxygen.cmake -------------------------------------------------------------------------------- /cmake/Format.cmake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cmake/Format.cmake -------------------------------------------------------------------------------- /cmake/GitVersion.cmake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cmake/GitVersion.cmake -------------------------------------------------------------------------------- /cmake/Packaging.cmake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cmake/Packaging.cmake -------------------------------------------------------------------------------- /cmake/Tests.cmake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cmake/Tests.cmake -------------------------------------------------------------------------------- /cmake/Utils.cmake: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cmake/Utils.cmake -------------------------------------------------------------------------------- /common/base/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/CMakeLists.txt -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/gw_config.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/gw_config.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/logging/logging.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/logging/logging.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/types.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/types.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/allocator.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/allocator.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/cudasort.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/cudasort.cuh -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/cudautils.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/cudautils.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/device_buffer.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/device_buffer.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/device_preallocated_allocator.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/device_preallocated_allocator.cuh -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/exceptions.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/exceptions.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/genomeutils.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/genomeutils.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/graph.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/graph.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/limits.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/limits.cuh -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/mathutils.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/mathutils.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/pinned_host_vector.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/pinned_host_vector.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/signed_integer_utils.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/signed_integer_utils.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/stringutils.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/stringutils.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/utils/threadsafe_containers.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/utils/threadsafe_containers.hpp -------------------------------------------------------------------------------- /common/base/include/claraparabricks/genomeworks/version.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/include/claraparabricks/genomeworks/version.hpp -------------------------------------------------------------------------------- /common/base/src/cudautils.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/src/cudautils.cpp -------------------------------------------------------------------------------- /common/base/src/graph.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/src/graph.cpp -------------------------------------------------------------------------------- /common/base/src/logging.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/src/logging.cpp -------------------------------------------------------------------------------- /common/base/src/version.cpp.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/src/version.cpp.in -------------------------------------------------------------------------------- /common/base/tests/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/tests/CMakeLists.txt -------------------------------------------------------------------------------- /common/base/tests/TestGraph.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/tests/TestGraph.cpp -------------------------------------------------------------------------------- /common/base/tests/Test_DevicePreallocatedAllocator.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/tests/Test_DevicePreallocatedAllocator.cu -------------------------------------------------------------------------------- /common/base/tests/Test_GenomeUtils.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/tests/Test_GenomeUtils.cpp -------------------------------------------------------------------------------- /common/base/tests/Test_UtilsCudasort.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/tests/Test_UtilsCudasort.cu -------------------------------------------------------------------------------- /common/base/tests/Test_UtilsThreadsafeContainers.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/tests/Test_UtilsThreadsafeContainers.cpp -------------------------------------------------------------------------------- /common/base/tests/main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/base/tests/main.cpp -------------------------------------------------------------------------------- /common/io/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/io/CMakeLists.txt -------------------------------------------------------------------------------- /common/io/include/claraparabricks/genomeworks/io/fasta_parser.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/io/include/claraparabricks/genomeworks/io/fasta_parser.hpp -------------------------------------------------------------------------------- /common/io/src/fasta_parser.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/io/src/fasta_parser.cpp -------------------------------------------------------------------------------- /common/io/src/kseqpp_fasta_parser.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/io/src/kseqpp_fasta_parser.cpp -------------------------------------------------------------------------------- /common/io/src/kseqpp_fasta_parser.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/common/io/src/kseqpp_fasta_parser.hpp -------------------------------------------------------------------------------- /cudaaligner/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/CMakeLists.txt -------------------------------------------------------------------------------- /cudaaligner/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/README.md -------------------------------------------------------------------------------- /cudaaligner/benchmarks/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/benchmarks/CMakeLists.txt -------------------------------------------------------------------------------- /cudaaligner/benchmarks/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/benchmarks/README.md -------------------------------------------------------------------------------- /cudaaligner/benchmarks/main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/benchmarks/main.cpp -------------------------------------------------------------------------------- /cudaaligner/include/claraparabricks/genomeworks/cudaaligner/aligner.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/include/claraparabricks/genomeworks/cudaaligner/aligner.hpp -------------------------------------------------------------------------------- /cudaaligner/include/claraparabricks/genomeworks/cudaaligner/alignment.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/include/claraparabricks/genomeworks/cudaaligner/alignment.hpp -------------------------------------------------------------------------------- /cudaaligner/include/claraparabricks/genomeworks/cudaaligner/cudaaligner.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/include/claraparabricks/genomeworks/cudaaligner/cudaaligner.hpp -------------------------------------------------------------------------------- /cudaaligner/samples/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/samples/CMakeLists.txt -------------------------------------------------------------------------------- /cudaaligner/samples/sample_cudaaligner.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/samples/sample_cudaaligner.cpp -------------------------------------------------------------------------------- /cudaaligner/src/aligner.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/aligner.cpp -------------------------------------------------------------------------------- /cudaaligner/src/aligner_global.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/aligner_global.cpp -------------------------------------------------------------------------------- /cudaaligner/src/aligner_global.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/aligner_global.hpp -------------------------------------------------------------------------------- /cudaaligner/src/aligner_global_hirschberg_myers.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/aligner_global_hirschberg_myers.cpp -------------------------------------------------------------------------------- /cudaaligner/src/aligner_global_hirschberg_myers.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/aligner_global_hirschberg_myers.hpp -------------------------------------------------------------------------------- /cudaaligner/src/aligner_global_myers.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/aligner_global_myers.cpp -------------------------------------------------------------------------------- /cudaaligner/src/aligner_global_myers.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/aligner_global_myers.hpp -------------------------------------------------------------------------------- /cudaaligner/src/aligner_global_myers_banded.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/aligner_global_myers_banded.cpp -------------------------------------------------------------------------------- /cudaaligner/src/aligner_global_myers_banded.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/aligner_global_myers_banded.hpp -------------------------------------------------------------------------------- /cudaaligner/src/aligner_global_ukkonen.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/aligner_global_ukkonen.cpp -------------------------------------------------------------------------------- /cudaaligner/src/aligner_global_ukkonen.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/aligner_global_ukkonen.hpp -------------------------------------------------------------------------------- /cudaaligner/src/alignment.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/alignment.cpp -------------------------------------------------------------------------------- /cudaaligner/src/alignment_impl.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/alignment_impl.cpp -------------------------------------------------------------------------------- /cudaaligner/src/alignment_impl.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/alignment_impl.hpp -------------------------------------------------------------------------------- /cudaaligner/src/batched_device_matrices.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/batched_device_matrices.cuh -------------------------------------------------------------------------------- /cudaaligner/src/cudaaligner.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/cudaaligner.cpp -------------------------------------------------------------------------------- /cudaaligner/src/hirschberg_myers_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/hirschberg_myers_gpu.cu -------------------------------------------------------------------------------- /cudaaligner/src/hirschberg_myers_gpu.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/hirschberg_myers_gpu.cuh -------------------------------------------------------------------------------- /cudaaligner/src/matrix_cpu.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/matrix_cpu.hpp -------------------------------------------------------------------------------- /cudaaligner/src/myers_cpu.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/myers_cpu.hpp -------------------------------------------------------------------------------- /cudaaligner/src/myers_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/myers_gpu.cu -------------------------------------------------------------------------------- /cudaaligner/src/myers_gpu.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/myers_gpu.cuh -------------------------------------------------------------------------------- /cudaaligner/src/needleman_wunsch_cpu.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/needleman_wunsch_cpu.cpp -------------------------------------------------------------------------------- /cudaaligner/src/needleman_wunsch_cpu.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/needleman_wunsch_cpu.hpp -------------------------------------------------------------------------------- /cudaaligner/src/ukkonen_cpu.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/ukkonen_cpu.cpp -------------------------------------------------------------------------------- /cudaaligner/src/ukkonen_cpu.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/ukkonen_cpu.hpp -------------------------------------------------------------------------------- /cudaaligner/src/ukkonen_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/ukkonen_gpu.cu -------------------------------------------------------------------------------- /cudaaligner/src/ukkonen_gpu.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/src/ukkonen_gpu.cuh -------------------------------------------------------------------------------- /cudaaligner/tests/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/tests/CMakeLists.txt -------------------------------------------------------------------------------- /cudaaligner/tests/Test_AlignerGlobal.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/tests/Test_AlignerGlobal.cpp -------------------------------------------------------------------------------- /cudaaligner/tests/Test_AlignmentImpl.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/tests/Test_AlignmentImpl.cpp -------------------------------------------------------------------------------- /cudaaligner/tests/Test_ApproximateBandedMyers.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/tests/Test_ApproximateBandedMyers.cpp -------------------------------------------------------------------------------- /cudaaligner/tests/Test_HirschbergMyers.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/tests/Test_HirschbergMyers.cu -------------------------------------------------------------------------------- /cudaaligner/tests/Test_Misc.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/tests/Test_Misc.cpp -------------------------------------------------------------------------------- /cudaaligner/tests/Test_MyersAlgorithm.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/tests/Test_MyersAlgorithm.cu -------------------------------------------------------------------------------- /cudaaligner/tests/Test_NeedlemanWunschImplementation.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/tests/Test_NeedlemanWunschImplementation.cpp -------------------------------------------------------------------------------- /cudaaligner/tests/cudaaligner_test_cases.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/tests/cudaaligner_test_cases.cpp -------------------------------------------------------------------------------- /cudaaligner/tests/cudaaligner_test_cases.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/tests/cudaaligner_test_cases.hpp -------------------------------------------------------------------------------- /cudaaligner/tests/main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaaligner/tests/main.cpp -------------------------------------------------------------------------------- /cudaextender/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/CMakeLists.txt -------------------------------------------------------------------------------- /cudaextender/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/README.md -------------------------------------------------------------------------------- /cudaextender/data/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/data/CMakeLists.txt -------------------------------------------------------------------------------- /cudaextender/data/cudaextender_file_location.hpp.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/data/cudaextender_file_location.hpp.in -------------------------------------------------------------------------------- /cudaextender/data/sample.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/data/sample.fa -------------------------------------------------------------------------------- /cudaextender/data/sample_scored_segment_pairs.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/data/sample_scored_segment_pairs.csv -------------------------------------------------------------------------------- /cudaextender/data/sample_seed_pairs.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/data/sample_seed_pairs.csv -------------------------------------------------------------------------------- /cudaextender/include/claraparabricks/genomeworks/cudaextender/cudaextender.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/include/claraparabricks/genomeworks/cudaextender/cudaextender.hpp -------------------------------------------------------------------------------- /cudaextender/include/claraparabricks/genomeworks/cudaextender/extender.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/include/claraparabricks/genomeworks/cudaextender/extender.hpp -------------------------------------------------------------------------------- /cudaextender/include/claraparabricks/genomeworks/cudaextender/utils.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/include/claraparabricks/genomeworks/cudaextender/utils.hpp -------------------------------------------------------------------------------- /cudaextender/samples/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/samples/CMakeLists.txt -------------------------------------------------------------------------------- /cudaextender/samples/sample_cudaextender.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/samples/sample_cudaextender.cpp -------------------------------------------------------------------------------- /cudaextender/src/cudaextender.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/src/cudaextender.cpp -------------------------------------------------------------------------------- /cudaextender/src/extender.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/src/extender.cpp -------------------------------------------------------------------------------- /cudaextender/src/ungapped_xdrop.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/src/ungapped_xdrop.cu -------------------------------------------------------------------------------- /cudaextender/src/ungapped_xdrop.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/src/ungapped_xdrop.cuh -------------------------------------------------------------------------------- /cudaextender/src/ungapped_xdrop_kernels.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/src/ungapped_xdrop_kernels.cu -------------------------------------------------------------------------------- /cudaextender/src/ungapped_xdrop_kernels.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/src/ungapped_xdrop_kernels.cuh -------------------------------------------------------------------------------- /cudaextender/tests/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/tests/CMakeLists.txt -------------------------------------------------------------------------------- /cudaextender/tests/Test_CudaextenderEnd2End.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/tests/Test_CudaextenderEnd2End.cu -------------------------------------------------------------------------------- /cudaextender/tests/main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudaextender/tests/main.cpp -------------------------------------------------------------------------------- /cudamapper/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/CMakeLists.txt -------------------------------------------------------------------------------- /cudamapper/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/README.md -------------------------------------------------------------------------------- /cudamapper/data/10_reads.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/data/10_reads.fasta -------------------------------------------------------------------------------- /cudamapper/data/20_reads.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/data/20_reads.fasta -------------------------------------------------------------------------------- /cudamapper/data/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/data/CMakeLists.txt -------------------------------------------------------------------------------- /cudamapper/data/aaaactgaa_gccaaag.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/data/aaaactgaa_gccaaag.fasta -------------------------------------------------------------------------------- /cudamapper/data/aaaactgaa_gccaaag.fasta.fai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/data/aaaactgaa_gccaaag.fasta.fai -------------------------------------------------------------------------------- /cudamapper/data/aagcta.fasta: -------------------------------------------------------------------------------- 1 | >read_0 2 | AAGCTA 3 | -------------------------------------------------------------------------------- /cudamapper/data/catcaag.fasta: -------------------------------------------------------------------------------- 1 | >read_0 2 | CATCAAG 3 | -------------------------------------------------------------------------------- /cudamapper/data/catcaag_aagcta.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/data/catcaag_aagcta.fasta -------------------------------------------------------------------------------- /cudamapper/data/catcaag_aagcta.fasta.fai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/data/catcaag_aagcta.fasta.fai -------------------------------------------------------------------------------- /cudamapper/data/cccatacc.fasta: -------------------------------------------------------------------------------- 1 | >read_0 2 | CCCATACC 3 | -------------------------------------------------------------------------------- /cudamapper/data/cccatacc.fasta.fai: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/data/cccatacc.fasta.fai -------------------------------------------------------------------------------- /cudamapper/data/covid-reads.fasta.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/data/covid-reads.fasta.gz -------------------------------------------------------------------------------- /cudamapper/data/cudamapper_file_location.hpp.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/data/cudamapper_file_location.hpp.in -------------------------------------------------------------------------------- /cudamapper/data/gatt.fasta: -------------------------------------------------------------------------------- 1 | >read_0 2 | GATT 3 | -------------------------------------------------------------------------------- /cudamapper/data/gatt.fasta.fai: -------------------------------------------------------------------------------- 1 | read_0 4 8 4 5 2 | -------------------------------------------------------------------------------- /cudamapper/include/claraparabricks/genomeworks/cudamapper/cudamapper.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/include/claraparabricks/genomeworks/cudamapper/cudamapper.hpp -------------------------------------------------------------------------------- /cudamapper/include/claraparabricks/genomeworks/cudamapper/index.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/include/claraparabricks/genomeworks/cudamapper/index.hpp -------------------------------------------------------------------------------- /cudamapper/include/claraparabricks/genomeworks/cudamapper/matcher.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/include/claraparabricks/genomeworks/cudamapper/matcher.hpp -------------------------------------------------------------------------------- /cudamapper/include/claraparabricks/genomeworks/cudamapper/overlapper.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/include/claraparabricks/genomeworks/cudamapper/overlapper.hpp -------------------------------------------------------------------------------- /cudamapper/include/claraparabricks/genomeworks/cudamapper/sketch_element.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/include/claraparabricks/genomeworks/cudamapper/sketch_element.hpp -------------------------------------------------------------------------------- /cudamapper/include/claraparabricks/genomeworks/cudamapper/types.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/include/claraparabricks/genomeworks/cudamapper/types.hpp -------------------------------------------------------------------------------- /cudamapper/include/claraparabricks/genomeworks/cudamapper/utils.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/include/claraparabricks/genomeworks/cudamapper/utils.hpp -------------------------------------------------------------------------------- /cudamapper/samples/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/samples/CMakeLists.txt -------------------------------------------------------------------------------- /cudamapper/samples/sample_cudamapper.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/samples/sample_cudamapper.cpp -------------------------------------------------------------------------------- /cudamapper/src/application_parameters.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/application_parameters.cpp -------------------------------------------------------------------------------- /cudamapper/src/application_parameters.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/application_parameters.hpp -------------------------------------------------------------------------------- /cudamapper/src/cudamapper.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/cudamapper.cpp -------------------------------------------------------------------------------- /cudamapper/src/cudamapper_utils.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/cudamapper_utils.cpp -------------------------------------------------------------------------------- /cudamapper/src/cudamapper_utils.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/cudamapper_utils.hpp -------------------------------------------------------------------------------- /cudamapper/src/index.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/index.cu -------------------------------------------------------------------------------- /cudamapper/src/index_batcher.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/index_batcher.cu -------------------------------------------------------------------------------- /cudamapper/src/index_batcher.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/index_batcher.cuh -------------------------------------------------------------------------------- /cudamapper/src/index_cache.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/index_cache.cu -------------------------------------------------------------------------------- /cudamapper/src/index_cache.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/index_cache.cuh -------------------------------------------------------------------------------- /cudamapper/src/index_descriptor.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/index_descriptor.cpp -------------------------------------------------------------------------------- /cudamapper/src/index_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/index_gpu.cu -------------------------------------------------------------------------------- /cudamapper/src/index_gpu.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/index_gpu.cuh -------------------------------------------------------------------------------- /cudamapper/src/index_host_copy.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/index_host_copy.cu -------------------------------------------------------------------------------- /cudamapper/src/index_host_copy.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/index_host_copy.cuh -------------------------------------------------------------------------------- /cudamapper/src/main.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/main.cu -------------------------------------------------------------------------------- /cudamapper/src/matcher.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/matcher.cu -------------------------------------------------------------------------------- /cudamapper/src/matcher_gpu.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/matcher_gpu.cu -------------------------------------------------------------------------------- /cudamapper/src/matcher_gpu.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/matcher_gpu.cuh -------------------------------------------------------------------------------- /cudamapper/src/minimizer.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/minimizer.cu -------------------------------------------------------------------------------- /cudamapper/src/minimizer.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/minimizer.hpp -------------------------------------------------------------------------------- /cudamapper/src/overlapper.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/overlapper.cpp -------------------------------------------------------------------------------- /cudamapper/src/overlapper_triggered.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/overlapper_triggered.cu -------------------------------------------------------------------------------- /cudamapper/src/overlapper_triggered.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/overlapper_triggered.hpp -------------------------------------------------------------------------------- /cudamapper/src/utils.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/src/utils.cpp -------------------------------------------------------------------------------- /cudamapper/tests/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/tests/CMakeLists.txt -------------------------------------------------------------------------------- /cudamapper/tests/Test_CudamapperIndexBatcher.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/tests/Test_CudamapperIndexBatcher.cu -------------------------------------------------------------------------------- /cudamapper/tests/Test_CudamapperIndexCache.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/tests/Test_CudamapperIndexCache.cu -------------------------------------------------------------------------------- /cudamapper/tests/Test_CudamapperIndexDescriptor.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/tests/Test_CudamapperIndexDescriptor.cpp -------------------------------------------------------------------------------- /cudamapper/tests/Test_CudamapperIndexGPU.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/tests/Test_CudamapperIndexGPU.cu -------------------------------------------------------------------------------- /cudamapper/tests/Test_CudamapperMatcherGPU.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/tests/Test_CudamapperMatcherGPU.cu -------------------------------------------------------------------------------- /cudamapper/tests/Test_CudamapperMinimizer.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/tests/Test_CudamapperMinimizer.cpp -------------------------------------------------------------------------------- /cudamapper/tests/Test_CudamapperOverlapper.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/tests/Test_CudamapperOverlapper.cpp -------------------------------------------------------------------------------- /cudamapper/tests/Test_CudamapperOverlapperTriggered.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/tests/Test_CudamapperOverlapperTriggered.cu -------------------------------------------------------------------------------- /cudamapper/tests/Test_CudamapperUtilsKmerFunctions.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/tests/Test_CudamapperUtilsKmerFunctions.cpp -------------------------------------------------------------------------------- /cudamapper/tests/main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/tests/main.cpp -------------------------------------------------------------------------------- /cudamapper/tests/mock_fasta_parser.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/tests/mock_fasta_parser.hpp -------------------------------------------------------------------------------- /cudamapper/tests/mock_index.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudamapper/tests/mock_index.cuh -------------------------------------------------------------------------------- /cudapoa/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/CMakeLists.txt -------------------------------------------------------------------------------- /cudapoa/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/README.md -------------------------------------------------------------------------------- /cudapoa/benchmarks/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/benchmarks/CMakeLists.txt -------------------------------------------------------------------------------- /cudapoa/benchmarks/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/benchmarks/README.md -------------------------------------------------------------------------------- /cudapoa/benchmarks/main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/benchmarks/main.cpp -------------------------------------------------------------------------------- /cudapoa/benchmarks/multi_batch.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/benchmarks/multi_batch.hpp -------------------------------------------------------------------------------- /cudapoa/benchmarks/single_batch.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/benchmarks/single_batch.hpp -------------------------------------------------------------------------------- /cudapoa/data/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/data/CMakeLists.txt -------------------------------------------------------------------------------- /cudapoa/data/file_location.hpp.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/data/file_location.hpp.in -------------------------------------------------------------------------------- /cudapoa/data/sample-bonito.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/data/sample-bonito.txt -------------------------------------------------------------------------------- /cudapoa/data/sample-golden-value.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/data/sample-golden-value.txt -------------------------------------------------------------------------------- /cudapoa/data/sample-windows.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/data/sample-windows.txt -------------------------------------------------------------------------------- /cudapoa/include/claraparabricks/genomeworks/cudapoa/batch.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/include/claraparabricks/genomeworks/cudapoa/batch.hpp -------------------------------------------------------------------------------- /cudapoa/include/claraparabricks/genomeworks/cudapoa/cudapoa.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/include/claraparabricks/genomeworks/cudapoa/cudapoa.hpp -------------------------------------------------------------------------------- /cudapoa/include/claraparabricks/genomeworks/cudapoa/utils.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/include/claraparabricks/genomeworks/cudapoa/utils.hpp -------------------------------------------------------------------------------- /cudapoa/samples/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/samples/CMakeLists.txt -------------------------------------------------------------------------------- /cudapoa/samples/sample_cudapoa.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/samples/sample_cudapoa.cpp -------------------------------------------------------------------------------- /cudapoa/src/allocate_block.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/allocate_block.hpp -------------------------------------------------------------------------------- /cudapoa/src/application_parameters.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/application_parameters.cpp -------------------------------------------------------------------------------- /cudapoa/src/application_parameters.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/application_parameters.hpp -------------------------------------------------------------------------------- /cudapoa/src/batch.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/batch.cu -------------------------------------------------------------------------------- /cudapoa/src/cudapoa.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/cudapoa.cpp -------------------------------------------------------------------------------- /cudapoa/src/cudapoa_add_alignment.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/cudapoa_add_alignment.cuh -------------------------------------------------------------------------------- /cudapoa/src/cudapoa_batch.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/cudapoa_batch.cuh -------------------------------------------------------------------------------- /cudapoa/src/cudapoa_generate_consensus.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/cudapoa_generate_consensus.cuh -------------------------------------------------------------------------------- /cudapoa/src/cudapoa_generate_msa.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/cudapoa_generate_msa.cuh -------------------------------------------------------------------------------- /cudapoa/src/cudapoa_kernels.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/cudapoa_kernels.cuh -------------------------------------------------------------------------------- /cudapoa/src/cudapoa_limits.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/cudapoa_limits.hpp -------------------------------------------------------------------------------- /cudapoa/src/cudapoa_nw.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/cudapoa_nw.cuh -------------------------------------------------------------------------------- /cudapoa/src/cudapoa_nw_banded.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/cudapoa_nw_banded.cuh -------------------------------------------------------------------------------- /cudapoa/src/cudapoa_nw_tb_banded.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/cudapoa_nw_tb_banded.cuh -------------------------------------------------------------------------------- /cudapoa/src/cudapoa_structs.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/cudapoa_structs.cuh -------------------------------------------------------------------------------- /cudapoa/src/cudapoa_topsort.cuh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/cudapoa_topsort.cuh -------------------------------------------------------------------------------- /cudapoa/src/main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/main.cpp -------------------------------------------------------------------------------- /cudapoa/src/utils.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/src/utils.cu -------------------------------------------------------------------------------- /cudapoa/tests/CMakeLists.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/tests/CMakeLists.txt -------------------------------------------------------------------------------- /cudapoa/tests/Test_CudapoaAddAlignment.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/tests/Test_CudapoaAddAlignment.cu -------------------------------------------------------------------------------- /cudapoa/tests/Test_CudapoaBatch.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/tests/Test_CudapoaBatch.cu -------------------------------------------------------------------------------- /cudapoa/tests/Test_CudapoaBatchEnd2End.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/tests/Test_CudapoaBatchEnd2End.cu -------------------------------------------------------------------------------- /cudapoa/tests/Test_CudapoaGenerateConsensus.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/tests/Test_CudapoaGenerateConsensus.cu -------------------------------------------------------------------------------- /cudapoa/tests/Test_CudapoaGenerateMSA2.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/tests/Test_CudapoaGenerateMSA2.cu -------------------------------------------------------------------------------- /cudapoa/tests/Test_CudapoaNW.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/tests/Test_CudapoaNW.cu -------------------------------------------------------------------------------- /cudapoa/tests/Test_CudapoaSerializeGraph.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/tests/Test_CudapoaSerializeGraph.cpp -------------------------------------------------------------------------------- /cudapoa/tests/Test_CudapoaTopSort.cu: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/tests/Test_CudapoaTopSort.cu -------------------------------------------------------------------------------- /cudapoa/tests/basic_graph.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/tests/basic_graph.hpp -------------------------------------------------------------------------------- /cudapoa/tests/main.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/tests/main.cpp -------------------------------------------------------------------------------- /cudapoa/tests/sorted_graph.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/cudapoa/tests/sorted_graph.hpp -------------------------------------------------------------------------------- /docs/Doxyfile.in: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/docs/Doxyfile.in -------------------------------------------------------------------------------- /pygenomeworks/.flake8.cython: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/.flake8.cython -------------------------------------------------------------------------------- /pygenomeworks/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/README.md -------------------------------------------------------------------------------- /pygenomeworks/bin/alignment_visualizer: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/bin/alignment_visualizer -------------------------------------------------------------------------------- /pygenomeworks/bin/evaluate_paf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/bin/evaluate_paf -------------------------------------------------------------------------------- /pygenomeworks/bin/genome_simulator: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/bin/genome_simulator -------------------------------------------------------------------------------- /pygenomeworks/generate_docs: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/generate_docs -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/__init__.py -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/cuda/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/cuda/__init__.py -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/cuda/cuda.pxd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/cuda/cuda.pxd -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/cuda/cuda.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/cuda/cuda.pyx -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/cuda/cuda_runtime_api.pxd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/cuda/cuda_runtime_api.pxd -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/cudaaligner/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/cudaaligner/__init__.py -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/cudaaligner/cudaaligner.pxd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/cudaaligner/cudaaligner.pxd -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/cudaaligner/cudaaligner.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/cudaaligner/cudaaligner.pyx -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/cudapoa/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/cudapoa/__init__.py -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/cudapoa/cudapoa.pxd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/cudapoa/cudapoa.pxd -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/cudapoa/cudapoa.pyx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/cudapoa/cudapoa.pyx -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/cudapoa/graph.pxd: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/cudapoa/graph.pxd -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/io/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/io/__init__.py -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/io/fastaio.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/io/fastaio.py -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/io/pafio.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/io/pafio.py -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/io/utils.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/io/utils.py -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/simulators/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/simulators/__init__.py -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/simulators/genomesim.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/simulators/genomesim.py -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/simulators/readsim.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/simulators/readsim.py -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/utilities/__init__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/utilities/__init__.py -------------------------------------------------------------------------------- /pygenomeworks/genomeworks/utilities/utilities.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/genomeworks/utilities/utilities.py -------------------------------------------------------------------------------- /pygenomeworks/python-style-requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/python-style-requirements.txt -------------------------------------------------------------------------------- /pygenomeworks/requirements.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/requirements.txt -------------------------------------------------------------------------------- /pygenomeworks/samples/sample_cudaaligner: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/samples/sample_cudaaligner -------------------------------------------------------------------------------- /pygenomeworks/samples/sample_cudapoa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/samples/sample_cudapoa -------------------------------------------------------------------------------- /pygenomeworks/setup.cfg: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/setup.cfg -------------------------------------------------------------------------------- /pygenomeworks/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/setup.py -------------------------------------------------------------------------------- /pygenomeworks/setup_pygenomeworks.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/setup_pygenomeworks.py -------------------------------------------------------------------------------- /pygenomeworks/style_check: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/style_check -------------------------------------------------------------------------------- /pygenomeworks/test/data/assembly_GT.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/test/data/assembly_GT.fa -------------------------------------------------------------------------------- /pygenomeworks/test/data/assembly_GT.gfa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/test/data/assembly_GT.gfa -------------------------------------------------------------------------------- /pygenomeworks/test/data/overlaps_GT.paf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/test/data/overlaps_GT.paf -------------------------------------------------------------------------------- /pygenomeworks/test/data/overlaps_on_assembly_GT.paf: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/test/data/overlaps_on_assembly_GT.paf -------------------------------------------------------------------------------- /pygenomeworks/test/data/polished_assembly_CPU_subgraph_GT.fa: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/test/data/polished_assembly_CPU_subgraph_GT.fa -------------------------------------------------------------------------------- /pygenomeworks/test/data/reads.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/test/data/reads.fasta -------------------------------------------------------------------------------- /pygenomeworks/test/data/ref.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/test/data/ref.fasta -------------------------------------------------------------------------------- /pygenomeworks/test/test_cuda_bindings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/test/test_cuda_bindings.py -------------------------------------------------------------------------------- /pygenomeworks/test/test_cudaaligner_bindings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/test/test_cudaaligner_bindings.py -------------------------------------------------------------------------------- /pygenomeworks/test/test_cudapoa_bindings.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/test/test_cudapoa_bindings.py -------------------------------------------------------------------------------- /pygenomeworks/test/test_genome_simulator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/test/test_genome_simulator.py -------------------------------------------------------------------------------- /pygenomeworks/test/test_overlap_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/test/test_overlap_generator.py -------------------------------------------------------------------------------- /pygenomeworks/test/test_read_simulators.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/NVIDIA-Genomics-Research/GenomeWorks/HEAD/pygenomeworks/test/test_read_simulators.py --------------------------------------------------------------------------------