├── .gitignore ├── CMakeLists.txt ├── CODE_OF_CONDUCT.md ├── CONTRIBUTING.md ├── LICENSE ├── README.md ├── cmake └── Modules │ └── FindJemalloc.cmake ├── data ├── Datasets.md ├── cycles.fa ├── reads.fq ├── refs1.fa ├── refs1.lst ├── refs2.fa ├── refs2.lst ├── rob-palindrome.fa └── rob-palindrome.lst ├── include ├── Annotated_Kmer.hpp ├── Application.hpp ├── Async_Logger_Wrapper.hpp ├── BBHash │ ├── BooPHF.h │ └── LICENSE ├── Build_Params.hpp ├── CdBG.hpp ├── Character_Buffer.hpp ├── DNA.hpp ├── DNA_Utility.hpp ├── Data_Logistics.hpp ├── Directed_Kmer.hpp ├── Directed_Vertex.hpp ├── Edge.hpp ├── Endpoint.hpp ├── FASTA_Record.hpp ├── File_Extensions.hpp ├── Input_Defaults.hpp ├── Job_Queue.hpp ├── Kmer.hpp ├── Kmer_Buffered_Iterator.hpp ├── Kmer_Container.hpp ├── Kmer_Hash_Entry_API.hpp ├── Kmer_Hash_Table.hpp ├── Kmer_Hasher.hpp ├── Kmer_Iterator.hpp ├── Kmer_SPMC_Iterator.hpp ├── Kmer_Utility.hpp ├── Kmer_u64.hpp ├── Maximal_Unitig_Scratch.hpp ├── Minimizer_Policy.hpp ├── Oriented_Unitig.hpp ├── Output_Format.hpp ├── Output_Sink.hpp ├── Progress_Tracker.hpp ├── Read_CdBG.hpp ├── Read_CdBG_Constructor.hpp ├── Read_CdBG_Extractor.hpp ├── Ref_Parser.hpp ├── Seq_Input.hpp ├── Sparse_Lock.hpp ├── Spin_Lock.hpp ├── State.hpp ├── State_Read_Space.hpp ├── Task_Params.hpp ├── Thread_Pool.hpp ├── Unipaths_Meta_info.hpp ├── Unitig_Scratch.hpp ├── Validation_Params.hpp ├── Validator.hpp ├── Vertex.hpp ├── boost │ ├── LICENSE_1_0.txt │ └── preprocessor │ │ ├── arithmetic.hpp │ │ ├── arithmetic │ │ ├── add.hpp │ │ ├── dec.hpp │ │ ├── detail │ │ │ └── div_base.hpp │ │ ├── div.hpp │ │ ├── inc.hpp │ │ ├── mod.hpp │ │ ├── mul.hpp │ │ └── sub.hpp │ │ ├── array.hpp │ │ ├── array │ │ ├── data.hpp │ │ ├── detail │ │ │ └── get_data.hpp │ │ ├── elem.hpp │ │ ├── enum.hpp │ │ ├── insert.hpp │ │ ├── pop_back.hpp │ │ ├── pop_front.hpp │ │ ├── push_back.hpp │ │ ├── push_front.hpp │ │ ├── remove.hpp │ │ ├── replace.hpp │ │ ├── reverse.hpp │ │ ├── size.hpp │ │ ├── to_list.hpp │ │ ├── to_seq.hpp │ │ └── to_tuple.hpp │ │ ├── assert_msg.hpp │ │ ├── cat.hpp │ │ ├── comma.hpp │ │ ├── comma_if.hpp │ │ ├── comparison.hpp │ │ ├── comparison │ │ ├── equal.hpp │ │ ├── greater.hpp │ │ ├── greater_equal.hpp │ │ ├── less.hpp │ │ ├── less_equal.hpp │ │ └── not_equal.hpp │ │ ├── config │ │ ├── config.hpp │ │ └── limits.hpp │ │ ├── control.hpp │ │ ├── control │ │ ├── deduce_d.hpp │ │ ├── detail │ │ │ ├── dmc │ │ │ │ └── while.hpp │ │ │ ├── edg │ │ │ │ └── while.hpp │ │ │ ├── msvc │ │ │ │ └── while.hpp │ │ │ └── while.hpp │ │ ├── expr_if.hpp │ │ ├── expr_iif.hpp │ │ ├── if.hpp │ │ ├── iif.hpp │ │ └── while.hpp │ │ ├── debug.hpp │ │ ├── debug │ │ ├── assert.hpp │ │ ├── error.hpp │ │ └── line.hpp │ │ ├── dec.hpp │ │ ├── detail │ │ ├── auto_rec.hpp │ │ ├── check.hpp │ │ ├── dmc │ │ │ └── auto_rec.hpp │ │ ├── is_binary.hpp │ │ ├── is_nullary.hpp │ │ ├── is_unary.hpp │ │ ├── null.hpp │ │ └── split.hpp │ │ ├── empty.hpp │ │ ├── enum.hpp │ │ ├── enum_params.hpp │ │ ├── enum_params_with_a_default.hpp │ │ ├── enum_params_with_defaults.hpp │ │ ├── enum_shifted.hpp │ │ ├── enum_shifted_params.hpp │ │ ├── expand.hpp │ │ ├── expr_if.hpp │ │ ├── facilities.hpp │ │ ├── facilities │ │ ├── apply.hpp │ │ ├── detail │ │ │ └── is_empty.hpp │ │ ├── empty.hpp │ │ ├── expand.hpp │ │ ├── identity.hpp │ │ ├── intercept.hpp │ │ ├── is_1.hpp │ │ ├── is_empty.hpp │ │ ├── is_empty_or_1.hpp │ │ ├── is_empty_variadic.hpp │ │ └── overload.hpp │ │ ├── for.hpp │ │ ├── identity.hpp │ │ ├── if.hpp │ │ ├── inc.hpp │ │ ├── iterate.hpp │ │ ├── iteration.hpp │ │ ├── iteration │ │ ├── detail │ │ │ ├── bounds │ │ │ │ ├── lower1.hpp │ │ │ │ ├── lower2.hpp │ │ │ │ ├── lower3.hpp │ │ │ │ ├── lower4.hpp │ │ │ │ ├── lower5.hpp │ │ │ │ ├── upper1.hpp │ │ │ │ ├── upper2.hpp │ │ │ │ ├── upper3.hpp │ │ │ │ ├── upper4.hpp │ │ │ │ └── upper5.hpp │ │ │ ├── finish.hpp │ │ │ ├── iter │ │ │ │ ├── forward1.hpp │ │ │ │ ├── forward2.hpp │ │ │ │ ├── forward3.hpp │ │ │ │ ├── forward4.hpp │ │ │ │ ├── forward5.hpp │ │ │ │ ├── reverse1.hpp │ │ │ │ ├── reverse2.hpp │ │ │ │ ├── reverse3.hpp │ │ │ │ ├── reverse4.hpp │ │ │ │ └── reverse5.hpp │ │ │ ├── local.hpp │ │ │ ├── rlocal.hpp │ │ │ ├── self.hpp │ │ │ └── start.hpp │ │ ├── iterate.hpp │ │ ├── local.hpp │ │ └── self.hpp │ │ ├── library.hpp │ │ ├── limits.hpp │ │ ├── list.hpp │ │ ├── list │ │ ├── adt.hpp │ │ ├── append.hpp │ │ ├── at.hpp │ │ ├── cat.hpp │ │ ├── detail │ │ │ ├── dmc │ │ │ │ └── fold_left.hpp │ │ │ ├── edg │ │ │ │ ├── fold_left.hpp │ │ │ │ └── fold_right.hpp │ │ │ ├── fold_left.hpp │ │ │ └── fold_right.hpp │ │ ├── enum.hpp │ │ ├── filter.hpp │ │ ├── first_n.hpp │ │ ├── fold_left.hpp │ │ ├── fold_right.hpp │ │ ├── for_each.hpp │ │ ├── for_each_i.hpp │ │ ├── for_each_product.hpp │ │ ├── rest_n.hpp │ │ ├── reverse.hpp │ │ ├── size.hpp │ │ ├── to_array.hpp │ │ ├── to_seq.hpp │ │ ├── to_tuple.hpp │ │ └── transform.hpp │ │ ├── logical.hpp │ │ ├── logical │ │ ├── and.hpp │ │ ├── bitand.hpp │ │ ├── bitnor.hpp │ │ ├── bitor.hpp │ │ ├── bitxor.hpp │ │ ├── bool.hpp │ │ ├── compl.hpp │ │ ├── nor.hpp │ │ ├── not.hpp │ │ ├── or.hpp │ │ └── xor.hpp │ │ ├── max.hpp │ │ ├── min.hpp │ │ ├── punctuation.hpp │ │ ├── punctuation │ │ ├── comma.hpp │ │ ├── comma_if.hpp │ │ ├── detail │ │ │ └── is_begin_parens.hpp │ │ ├── is_begin_parens.hpp │ │ ├── paren.hpp │ │ ├── paren_if.hpp │ │ └── remove_parens.hpp │ │ ├── repeat.hpp │ │ ├── repeat_2nd.hpp │ │ ├── repeat_3rd.hpp │ │ ├── repeat_from_to.hpp │ │ ├── repeat_from_to_2nd.hpp │ │ ├── repeat_from_to_3rd.hpp │ │ ├── repetition.hpp │ │ ├── repetition │ │ ├── deduce_r.hpp │ │ ├── deduce_z.hpp │ │ ├── detail │ │ │ ├── dmc │ │ │ │ └── for.hpp │ │ │ ├── edg │ │ │ │ └── for.hpp │ │ │ ├── for.hpp │ │ │ └── msvc │ │ │ │ └── for.hpp │ │ ├── enum.hpp │ │ ├── enum_binary_params.hpp │ │ ├── enum_params.hpp │ │ ├── enum_params_with_a_default.hpp │ │ ├── enum_params_with_defaults.hpp │ │ ├── enum_shifted.hpp │ │ ├── enum_shifted_binary_params.hpp │ │ ├── enum_shifted_params.hpp │ │ ├── enum_trailing.hpp │ │ ├── enum_trailing_binary_params.hpp │ │ ├── enum_trailing_params.hpp │ │ ├── for.hpp │ │ ├── repeat.hpp │ │ └── repeat_from_to.hpp │ │ ├── selection.hpp │ │ ├── selection │ │ ├── max.hpp │ │ └── min.hpp │ │ ├── seq.hpp │ │ ├── seq │ │ ├── cat.hpp │ │ ├── detail │ │ │ ├── binary_transform.hpp │ │ │ ├── is_empty.hpp │ │ │ ├── split.hpp │ │ │ └── to_list_msvc.hpp │ │ ├── elem.hpp │ │ ├── enum.hpp │ │ ├── filter.hpp │ │ ├── first_n.hpp │ │ ├── fold_left.hpp │ │ ├── fold_right.hpp │ │ ├── for_each.hpp │ │ ├── for_each_i.hpp │ │ ├── for_each_product.hpp │ │ ├── insert.hpp │ │ ├── pop_back.hpp │ │ ├── pop_front.hpp │ │ ├── push_back.hpp │ │ ├── push_front.hpp │ │ ├── remove.hpp │ │ ├── replace.hpp │ │ ├── rest_n.hpp │ │ ├── reverse.hpp │ │ ├── seq.hpp │ │ ├── size.hpp │ │ ├── subseq.hpp │ │ ├── to_array.hpp │ │ ├── to_list.hpp │ │ ├── to_tuple.hpp │ │ ├── transform.hpp │ │ └── variadic_seq_to_seq.hpp │ │ ├── slot.hpp │ │ ├── slot │ │ ├── counter.hpp │ │ ├── detail │ │ │ ├── counter.hpp │ │ │ ├── def.hpp │ │ │ ├── shared.hpp │ │ │ ├── slot1.hpp │ │ │ ├── slot2.hpp │ │ │ ├── slot3.hpp │ │ │ ├── slot4.hpp │ │ │ └── slot5.hpp │ │ └── slot.hpp │ │ ├── stringize.hpp │ │ ├── tuple.hpp │ │ ├── tuple │ │ ├── detail │ │ │ └── is_single_return.hpp │ │ ├── eat.hpp │ │ ├── elem.hpp │ │ ├── enum.hpp │ │ ├── insert.hpp │ │ ├── pop_back.hpp │ │ ├── pop_front.hpp │ │ ├── push_back.hpp │ │ ├── push_front.hpp │ │ ├── rem.hpp │ │ ├── remove.hpp │ │ ├── replace.hpp │ │ ├── reverse.hpp │ │ ├── size.hpp │ │ ├── to_array.hpp │ │ ├── to_list.hpp │ │ └── to_seq.hpp │ │ ├── variadic.hpp │ │ ├── variadic │ │ ├── detail │ │ │ └── is_single_return.hpp │ │ ├── elem.hpp │ │ ├── size.hpp │ │ ├── to_array.hpp │ │ ├── to_list.hpp │ │ ├── to_seq.hpp │ │ └── to_tuple.hpp │ │ ├── while.hpp │ │ └── wstringize.hpp ├── compact_vector │ ├── LICENSE │ ├── compact_iterator.hpp │ ├── compact_vector.hpp │ ├── const_iterator_traits.hpp │ ├── parallel_iterator_traits.hpp │ └── prefetch_iterator_traits.hpp ├── cxxopts │ ├── LICENSE │ └── cxxopts.hpp ├── dBG_Info.hpp ├── dBG_Utilities.hpp ├── fmt │ ├── LICENSE.rst │ ├── chrono.h │ ├── color.h │ ├── compile.h │ ├── core.h │ ├── format-inl.h │ ├── format.h │ ├── locale.h │ ├── os.h │ ├── ostream.h │ ├── posix.h │ ├── printf.h │ └── ranges.h ├── globals.hpp ├── kmc_api │ ├── Virtual_Prefix_File.hpp │ ├── kmc_file.h │ ├── kmer_api.h │ ├── kmer_defs.h │ ├── mmer.h │ └── stdafx.h ├── kmer_Enumeration_Stats.hpp ├── kmer_Enumerator.hpp ├── kseq │ └── kseq.h ├── nlohmann │ ├── LICENSE.MIT │ └── json.hpp ├── spdlog │ ├── LICENSE │ ├── async.h │ ├── async_logger-inl.h │ ├── async_logger.h │ ├── cfg │ │ ├── argv.h │ │ ├── env.h │ │ ├── helpers-inl.h │ │ ├── helpers.h │ │ └── log_levels.h │ ├── common-inl.h │ ├── common.h │ ├── details │ │ ├── backtracer-inl.h │ │ ├── backtracer.h │ │ ├── circular_q.h │ │ ├── console_globals.h │ │ ├── file_helper-inl.h │ │ ├── file_helper.h │ │ ├── fmt_helper.h │ │ ├── log_msg-inl.h │ │ ├── log_msg.h │ │ ├── log_msg_buffer-inl.h │ │ ├── log_msg_buffer.h │ │ ├── mpmc_blocking_q.h │ │ ├── null_mutex.h │ │ ├── os-inl.h │ │ ├── os.h │ │ ├── periodic_worker-inl.h │ │ ├── periodic_worker.h │ │ ├── registry-inl.h │ │ ├── registry.h │ │ ├── synchronous_factory.h │ │ ├── tcp_client-windows.h │ │ ├── tcp_client.h │ │ ├── thread_pool-inl.h │ │ ├── thread_pool.h │ │ └── windows_include.h │ ├── fmt │ │ ├── bin_to_hex.h │ │ ├── bundled │ │ │ ├── LICENSE.rst │ │ │ ├── chrono.h │ │ │ ├── color.h │ │ │ ├── compile.h │ │ │ ├── core.h │ │ │ ├── format-inl.h │ │ │ ├── format.h │ │ │ ├── locale.h │ │ │ ├── ostream.h │ │ │ ├── posix.h │ │ │ ├── printf.h │ │ │ └── ranges.h │ │ ├── fmt.h │ │ └── ostr.h │ ├── formatter.h │ ├── fwd.h │ ├── logger-inl.h │ ├── logger.h │ ├── pattern_formatter-inl.h │ ├── pattern_formatter.h │ ├── sinks │ │ ├── android_sink.h │ │ ├── ansicolor_sink-inl.h │ │ ├── ansicolor_sink.h │ │ ├── base_sink-inl.h │ │ ├── base_sink.h │ │ ├── basic_file_sink-inl.h │ │ ├── basic_file_sink.h │ │ ├── daily_file_sink.h │ │ ├── dist_sink.h │ │ ├── dup_filter_sink.h │ │ ├── msvc_sink.h │ │ ├── null_sink.h │ │ ├── ostream_sink.h │ │ ├── ringbuffer_sink.h │ │ ├── rotating_file_sink-inl.h │ │ ├── rotating_file_sink.h │ │ ├── sink-inl.h │ │ ├── sink.h │ │ ├── stdout_color_sinks-inl.h │ │ ├── stdout_color_sinks.h │ │ ├── stdout_sinks-inl.h │ │ ├── stdout_sinks.h │ │ ├── syslog_sink.h │ │ ├── systemd_sink.h │ │ ├── tcp_sink.h │ │ ├── win_eventlog_sink.h │ │ ├── wincolor_sink-inl.h │ │ └── wincolor_sink.h │ ├── spdlog-inl.h │ ├── spdlog.h │ ├── tweakme.h │ └── version.h ├── utility.hpp ├── version.hpp └── xxHash │ ├── LICENSE │ ├── xxh3.h │ └── xxhash.h ├── patches ├── kmc-v3.2.1_cuttlefish-dev.diff └── kmc_patch.diff ├── scripts ├── merge_into_develop.sh └── merge_into_master.sh └── src ├── Application.cpp ├── Async_Logger_Wrapper.cpp ├── Build_Params.cpp ├── CMakeLists.txt ├── CdBG.cpp ├── CdBG_Builder.cpp ├── CdBG_GFA_Reduced_Writer.cpp ├── CdBG_GFA_Writer.cpp ├── CdBG_Plain_Writer.cpp ├── CdBG_Writer.cpp ├── Character_Buffer_Flusher.cpp ├── DNA_Utility.cpp ├── Data_Logistics.cpp ├── Kmer_Container.cpp ├── Kmer_Hash_Table.cpp ├── Kmer_Utility.cpp ├── Kmer_u64.cpp ├── Kmers_Validator.cpp ├── Maximal_Unitig_Scratch.cpp ├── Minimizer_Policy.cpp ├── Obsolete ├── Detached_Cycles_Extractor.cpp ├── Read_CdBG_Constructor_Obsolete.cpp ├── Read_CdBG_Extractor_Obsolete.cpp └── Read_CdBG_Obsolete.cpp ├── Progress_Tracker.cpp ├── Read_CdBG.cpp ├── Read_CdBG_Constructor.cpp ├── Read_CdBG_Extractor.cpp ├── Ref_Parser.cpp ├── Seq_Input.cpp ├── Sequence_Validator.cpp ├── State.cpp ├── State_Read_Space.cpp ├── Thread_Pool.cpp ├── Unipaths_Meta_info.cpp ├── Unitig_Scratch.cpp ├── Validator.cpp ├── Validator_Hash_Table.cpp ├── Vertex.cpp ├── commands.cpp ├── dBG_Info.cpp ├── dBG_Utilities.cpp ├── kmc_api ├── Virtual_Prefix_File.cpp ├── kmc_file.cpp ├── kmer_api.cpp └── mmer.cpp ├── kmer_Enumeration_Stats.cpp ├── kmer_Enumerator.cpp ├── main.cpp ├── test.cpp ├── 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