├── .gitignore ├── .gitmodules ├── .travis.yml ├── CMakeLists.txt ├── Dockerfile ├── LICENSE ├── README.md ├── common ├── DRAM.cpp ├── DRAM.h ├── cuda_utils.h ├── kseq.h ├── ntcoding.cpp ├── ntcoding.h ├── parameters.h ├── seed_filter_interface.cu ├── seed_filter_interface.h ├── seed_pos_table.cu └── store_gpu.h ├── logo.png ├── repeat_masker_src ├── graph.h ├── main.cpp ├── seed_filter.cu ├── seed_filter.h ├── seeder.cpp ├── segment_printer.cpp └── store.h ├── scripts ├── installUbuntu.sh ├── run_segalign └── run_segalign_repeat_masker └── src ├── graph.h ├── main.cpp ├── seed_filter.cu ├── seed_filter.h ├── seeder.cpp ├── segment_printer.cpp └── store.h /.gitignore: -------------------------------------------------------------------------------- 1 | build/ 2 | test/ 3 | bin/ 4 | -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- 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