├── .github └── workflows │ └── build_and_test_on_push.yml ├── .gitignore ├── .gitmodules ├── CMakeLists.txt ├── Dockerfile ├── LICENSE ├── README.md ├── data └── HLA │ ├── A-3105.fa.gz │ ├── B-3106.fa.gz │ ├── C-3107.fa.gz │ ├── DMA-3108.fa.gz │ ├── DMB-3109.fa.gz │ ├── DOA-3111.fa.gz │ ├── DOB-3112.fa.gz │ ├── DPA1-3113.fa.gz │ ├── DPB1-3115.fa.gz │ ├── DQA1-3117.fa.gz │ ├── DQB1-3119.fa.gz │ ├── DRA-3122.fa.gz │ ├── DRB1-3123.fa.gz │ ├── DRB3-3125.fa.gz │ ├── DRB4-3126.fa.gz │ ├── DRB5-3127.fa.gz │ ├── E-3133.fa.gz │ ├── F-3134.fa.gz │ ├── G-3135.fa.gz │ ├── H-3136.fa.gz │ ├── J-3137.fa.gz │ ├── K-3138.fa.gz │ ├── L-3139.fa.gz │ ├── MICA-100507436.fa.gz │ ├── MICB-4277.fa.gz │ ├── TAP1-6890.fa.gz │ ├── TAP2-6891.fa.gz │ └── V-352962.fa.gz ├── default.nix ├── scripts ├── enum-pairs ├── generate_git_version.sh ├── pan-minimap2 ├── pan-self-minimap2 └── upper-triangle ├── seqwish.nix ├── src ├── alignments.cpp ├── alignments.hpp ├── cigar.cpp ├── cigar.hpp ├── compact.cpp ├── compact.hpp ├── dmultimap.hpp ├── dna.cpp ├── dna.hpp ├── dset64-gccAtomic.hpp ├── dset64.hpp ├── exists.cpp ├── exists.hpp ├── gfa.cpp ├── gfa.hpp ├── iitii_types.cpp ├── iitii_types.hpp ├── links.cpp ├── links.hpp ├── main.cpp ├── match.cpp ├── match.hpp ├── mmap.cpp ├── mmap.hpp ├── paf.cpp ├── paf.hpp ├── pos.cpp ├── pos.hpp ├── seqindex.cpp ├── seqindex.hpp ├── spinlock.hpp ├── sxs.cpp ├── sxs.hpp ├── tempfile.cpp ├── tempfile.hpp ├── time.cpp ├── time.hpp ├── tokenize.hpp ├── transclosure.cpp ├── transclosure.hpp ├── utils.cpp ├── utils.hpp ├── version.cpp ├── version.hpp ├── vgp.cpp ├── vgp.hpp └── wang.hpp └── test ├── HLA ├── A-3105.fa.gz ├── A-3105.fa.gz.gfa.md5 ├── A-3105.masked.fa.gz ├── A-3105.paf.gz ├── B-3106.fa.gz ├── B-3106.fa.gz.gfa.md5 ├── B-3106.paf.gz ├── C-3107.fa.gz ├── C-3107.fa.gz.gfa.md5 ├── C-3107.paf.gz ├── DMA-3108.fa.gz ├── DMA-3108.fa.gz.gfa.md5 ├── DMA-3108.paf.gz ├── DMB-3109.fa.gz ├── DMB-3109.fa.gz.gfa.md5 ├── DMB-3109.paf.gz ├── DOA-3111.fa.gz ├── DOA-3111.fa.gz.gfa.md5 ├── DOA-3111.paf.gz ├── DOB-3112.fa.gz ├── DOB-3112.fa.gz.gfa.md5 ├── DOB-3112.paf.gz ├── DPA1-3113.fa.gz ├── DPA1-3113.fa.gz.gfa.md5 ├── DPA1-3113.paf.gz ├── DPB1-3115.fa.gz ├── DPB1-3115.fa.gz.gfa.md5 ├── DPB1-3115.paf.gz ├── DQA1-3117.fa.gz ├── DQA1-3117.fa.gz.gfa.md5 ├── DQA1-3117.paf.gz ├── DQB1-3119.fa.gz ├── DQB1-3119.fa.gz.gfa.md5 ├── DQB1-3119.paf.gz ├── DRA-3122.fa.gz ├── DRA-3122.fa.gz.gfa.md5 ├── DRA-3122.paf.gz ├── DRB1-3123.fa.gz ├── DRB1-3123.fa.gz.gfa.md5 ├── DRB1-3123.paf.gz ├── DRB3-3125.fa.gz ├── DRB3-3125.fa.gz.gfa.md5 ├── DRB3-3125.paf.gz ├── DRB4-3126.fa.gz ├── DRB4-3126.fa.gz.gfa.md5 ├── DRB4-3126.paf.gz ├── DRB5-3127.fa.gz ├── DRB5-3127.fa.gz.gfa.md5 ├── DRB5-3127.paf.gz ├── E-3133.fa.gz ├── E-3133.fa.gz.gfa.md5 ├── E-3133.paf.gz ├── F-3134.fa.gz ├── F-3134.fa.gz.gfa.md5 ├── F-3134.paf.gz ├── G-3135.fa.gz ├── G-3135.fa.gz.gfa.md5 ├── G-3135.paf.gz ├── H-3136.fa.gz ├── H-3136.fa.gz.gfa.md5 ├── H-3136.paf.gz ├── J-3137.fa.gz ├── 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