├── .github ├── ISSUE_TEMPLATE │ └── bug_report.md └── workflows │ └── ci.yaml ├── CMakeLists.txt ├── LICENSE ├── README.md ├── SynDiv.py ├── SynDiv_c.cpp ├── SynDiv_p.py ├── genome2SynDiv_config.py ├── include ├── ChunkReader.hpp ├── Fst.hpp ├── GzChunkReader.hpp ├── SafeQueue.hpp ├── ThreadPool.hpp ├── cal.hpp ├── coor.hpp ├── fasta_length.py ├── file_open.py ├── get_time.hpp ├── kseq.h ├── multiinter.hpp ├── no_syn.hpp ├── no_syn_alignment.py ├── run_cmd.py ├── save.hpp ├── strip_split_join.hpp ├── syri_syn.py ├── sys.hpp └── window.hpp ├── meta.yaml ├── src ├── Fst.cpp ├── cal.cpp ├── coor.cpp ├── get_time.cpp ├── multiinter.cpp ├── no_syn.cpp ├── save.cpp ├── strip_split_join.cpp └── window.cpp └── test ├── aligns ├── An-1.aligns ├── C24.aligns ├── Cvi.aligns ├── Eri.aligns ├── Kyo.aligns ├── Ler.aligns └── Sha.aligns ├── code.sh ├── configuration.txt ├── genome ├── An-1.fa ├── An-1.fa.fai ├── C24.fa ├── C24.fa.fai ├── Cvi.fa ├── Cvi.fa.fai ├── Eri.fa ├── Eri.fa.fai ├── Kyo.fa ├── 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