├── CMakeLists.txt ├── MANIFEST.in ├── Makefile ├── README ├── README.md ├── bin ├── emeraLD └── emeraLD_pg ├── copyrights ├── COPYING └── LICENSE.txt ├── emeraLD2R.r ├── example.sh ├── example ├── chr20.1KG.25K_m.m3vcf.gz ├── chr20.1KG.25K_m.m3vcf.gz.tbi ├── chr20.1KG.25K_m.vcf.gz └── chr20.1KG.25K_m.vcf.gz.tbi ├── pybind11-init.sh ├── pybind11-merge.sh ├── setup.py └── src ├── LICENSES ├── Main.cpp ├── boost ├── LICENSE ├── assert.hpp ├── config.hpp ├── config │ ├── compiler │ │ ├── clang.hpp │ │ └── gcc.hpp │ ├── detail │ │ ├── posix_features.hpp │ │ ├── select_compiler_config.hpp │ │ ├── select_platform_config.hpp │ │ ├── select_stdlib_config.hpp │ │ └── suffix.hpp │ ├── helper_macros.hpp │ ├── platform │ │ ├── linux.hpp │ │ └── macos.hpp │ ├── stdlib │ │ ├── libcpp.hpp │ │ └── libstdcpp3.hpp │ ├── user.hpp │ └── workaround.hpp ├── core │ ├── addressof.hpp │ └── no_exceptions_support.hpp ├── current_function.hpp ├── detail │ ├── dynamic_bitset.hpp │ ├── iterator.hpp │ ├── no_exceptions_support.hpp │ └── workaround.hpp ├── dynamic_bitset.hpp ├── dynamic_bitset │ ├── config.hpp │ ├── dynamic_bitset.hpp │ └── serialization.hpp ├── dynamic_bitset_fwd.hpp ├── exception │ └── exception.hpp ├── integer │ └── integer_log2.hpp ├── limits.hpp ├── move │ ├── algo │ │ └── move.hpp │ ├── algorithm.hpp │ ├── core.hpp │ ├── detail │ │ ├── config_begin.hpp │ │ ├── config_end.hpp │ │ ├── iterator_to_raw_pointer.hpp │ │ ├── iterator_traits.hpp │ │ ├── meta_utils.hpp │ │ ├── meta_utils_core.hpp │ │ ├── pointer_element.hpp │ │ ├── std_ns_begin.hpp │ │ ├── std_ns_end.hpp │ │ ├── to_raw_pointer.hpp │ │ ├── type_traits.hpp │ │ └── workaround.hpp │ ├── iterator.hpp │ ├── move.hpp │ ├── traits.hpp │ ├── utility.hpp │ └── utility_core.hpp ├── pending │ └── lowest_bit.hpp ├── serialization │ ├── access.hpp │ ├── archive_input_unordered_map.hpp │ ├── archive_input_unordered_set.hpp │ ├── array.hpp │ ├── array_optimization.hpp │ ├── array_wrapper.hpp │ ├── assume_abstract.hpp │ ├── base_object.hpp │ ├── binary_object.hpp │ ├── bitset.hpp │ ├── boost_array.hpp │ ├── boost_unordered_map.hpp │ ├── boost_unordered_set.hpp │ ├── collection_size_type.hpp │ ├── collection_traits.hpp │ ├── collections_load_imp.hpp │ ├── collections_save_imp.hpp │ ├── complex.hpp │ ├── config.hpp │ ├── deque.hpp │ ├── detail │ │ ├── is_default_constructible.hpp │ │ ├── shared_count_132.hpp │ │ ├── shared_ptr_132.hpp │ │ ├── shared_ptr_nmt_132.hpp │ │ └── stack_constructor.hpp │ ├── ephemeral.hpp │ ├── export.hpp │ ├── extended_type_info.hpp │ ├── extended_type_info_no_rtti.hpp │ ├── extended_type_info_typeid.hpp │ ├── factory.hpp │ ├── force_include.hpp │ ├── forward_list.hpp │ ├── hash_collections_load_imp.hpp │ ├── hash_collections_save_imp.hpp │ ├── hash_map.hpp │ ├── hash_set.hpp │ ├── is_bitwise_serializable.hpp │ ├── item_version_type.hpp │ ├── level.hpp │ ├── level_enum.hpp │ ├── list.hpp │ ├── map.hpp │ ├── nvp.hpp │ ├── optional.hpp │ ├── priority_queue.hpp │ ├── queue.hpp │ ├── scoped_ptr.hpp │ ├── serialization.hpp │ ├── set.hpp │ ├── shared_ptr.hpp │ ├── shared_ptr_132.hpp │ ├── shared_ptr_helper.hpp │ ├── singleton.hpp │ ├── slist.hpp │ ├── smart_cast.hpp │ ├── split_free.hpp │ ├── split_member.hpp │ ├── stack.hpp │ ├── state_saver.hpp │ ├── static_warning.hpp │ ├── string.hpp │ ├── strong_typedef.hpp │ ├── throw_exception.hpp │ ├── tracking.hpp │ ├── tracking_enum.hpp │ ├── traits.hpp │ ├── type_info_implementation.hpp │ ├── unique_ptr.hpp │ ├── unordered_collections_load_imp.hpp │ ├── unordered_collections_save_imp.hpp │ ├── unordered_map.hpp │ ├── unordered_set.hpp │ ├── utility.hpp │ ├── valarray.hpp │ ├── variant.hpp │ ├── vector.hpp │ ├── vector_135.hpp │ ├── version.hpp │ ├── void_cast.hpp │ ├── void_cast_fwd.hpp │ ├── weak_ptr.hpp │ └── wrapper.hpp ├── static_assert.hpp ├── throw_exception.hpp └── utility │ └── addressof.hpp ├── calcLD.cpp ├── calcLD.hpp ├── emeraldpy ├── core.cpp ├── core.hpp └── wrap.cpp ├── htslib ├── LICENSE ├── bam_endian.h 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