├── LICENSE ├── README.md ├── example ├── 22.example.ref.vcf.gz ├── 22.example.ref.vcf.gz.csi ├── 22.example.vcf.gz ├── 22.example.vcf.gz.csi └── genetic_map_hg19_chr22.txt ├── extract_summary.awk ├── extract_summary_yaml.awk ├── launch_eagleimp ├── mergeX_info_yaml.awk ├── mergeX_message_yaml.awk └── src ├── Args.cpp ├── Args.h ├── Beam.cpp ├── Beam.h ├── BeamPath.cpp ├── BeamPath.h ├── BooleanHistory.cpp ├── BooleanHistory.h ├── CMakeLists.txt ├── CMakeModules ├── FindADMXRC3.cmake ├── FindHTSlib.cmake ├── FindNVML.cmake └── LibFindMacros.cmake ├── Datatypes.cpp ├── Datatypes.h ├── FPGAConfigurationEagleImp.cpp ├── FPGAConfigurationEagleImp.h ├── FPGAHandler.cpp ├── FPGAHandler.h ├── GPUEngine.cu ├── GPUEngine.h ├── GPUHandler.cpp ├── GPUHandler.h ├── GPUKernels.cu ├── GPUKernels.h ├── HaplotypeHistory.h ├── HaplotypePath.cpp ├── HaplotypePath.h ├── History.h ├── MapInterpolater.cpp ├── MapInterpolater.h ├── MinMaxHeap.h ├── MyMalloc.h ├── PBWT.cpp ├── PBWT.h ├── PBWTImputer.cpp ├── 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