├── LICENSE ├── Makefile ├── README.md ├── estimate.R ├── geva.cpp ├── hmm ├── hmm_emission_probs.txt └── hmm_initial_probs.txt └── src ├── age ├── Age.cpp ├── Age.hpp ├── AgeDensity.cpp ├── AgeDensity.hpp ├── AgeEstimate.cpp ├── AgeEstimate.hpp ├── AgeInfer.cpp └── AgeInfer.hpp ├── func ├── count_share.h ├── detect_share.h ├── ibd_by_pair.h ├── ibd_by_site.h ├── infer_age.h ├── join_bin.h ├── load_bin.h ├── load_gen.h ├── load_hap.h ├── load_hmm.h ├── load_map.h ├── load_share.h ├── load_sim.h ├── load_vcf.h ├── print_ibd.h └── select_share.h ├── gen ├── Gen.hpp ├── GenGrid.cpp ├── GenGrid.hpp ├── GenMap.cpp ├── GenMap.hpp ├── GenMarker.cpp ├── GenMarker.hpp ├── GenSample.cpp ├── GenSample.hpp ├── GenShare.cpp ├── GenShare.hpp ├── GenVariant.cpp └── GenVariant.hpp ├── ibd ├── IBD.hpp ├── IBD_DGT.cpp ├── IBD_DGT.hpp ├── IBD_FGT.cpp ├── IBD_FGT.hpp ├── IBD_HMM.cpp ├── IBD_HMM.hpp ├── IBD_SIM.cpp ├── IBD_SIM.hpp ├── IBDbyPair.cpp ├── IBDbyPair.hpp ├── IBDbySite.cpp └── IBDbySite.hpp ├── 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