├── .gitignore ├── .travis.yml ├── COPYING ├── ChangeLog ├── Makefile ├── NEWS.md ├── QSufSort.c ├── QSufSort.h ├── README-alt.md ├── README.md ├── bamlite.c ├── bamlite.h ├── bntseq.c ├── bntseq.h ├── bwa.1 ├── bwa.c ├── bwa.h ├── bwakit ├── README.md ├── bwa-postalt.js ├── run-HLA ├── run-bwamem ├── run-gen-ref ├── typeHLA-selctg.js ├── typeHLA.js └── typeHLA.sh ├── bwamem.c ├── bwamem.h ├── bwamem_extra.c ├── bwamem_pair.c ├── bwape.c ├── bwase.c ├── bwase.h ├── bwaseqio.c ├── bwashm.c ├── bwt.c ├── bwt.h ├── bwt_gen.c ├── bwt_lite.c ├── bwt_lite.h ├── bwtaln.c ├── bwtaln.h ├── bwtgap.c ├── bwtgap.h ├── bwtindex.c ├── bwtsw2.h ├── bwtsw2_aux.c ├── bwtsw2_chain.c ├── bwtsw2_core.c ├── bwtsw2_main.c ├── bwtsw2_pair.c ├── cuda ├── CUDAKernel_memmgnt.cu ├── CUDAKernel_memmgnt.cuh ├── batch_config.h ├── bntseq_CUDA.cu ├── bntseq_CUDA.cuh ├── bwa_CUDA.cu ├── bwa_CUDA.cuh ├── bwamem_GPU.cu ├── bwamem_GPU.cuh ├── bwt_CUDA.cu ├── bwt_CUDA.cuh ├── errHandler.cuh ├── kbtree_CUDA.cu ├── 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