├── .clang-format ├── .gitignore ├── .travis.yml ├── CHANGELOG.md ├── CMakeLists.txt ├── Dockerfile ├── LICENSE ├── README.md ├── azure-pipelines.yml ├── codecov.yml ├── src ├── assembly │ ├── all_algo.h │ ├── bubble_remover.cpp │ ├── bubble_remover.h │ ├── contig_output.cpp │ ├── contig_output.h │ ├── contig_stat.h │ ├── low_depth_remover.cpp │ ├── low_depth_remover.h │ ├── sdbg_pruning.cpp │ ├── sdbg_pruning.h │ ├── tip_remover.cpp │ ├── tip_remover.h │ ├── unitig_graph.cpp │ ├── unitig_graph.h │ ├── unitig_graph_vertex.h │ ├── weak_link_remover.cpp │ └── weak_link_remover.h ├── definitions.h ├── idba │ ├── README │ ├── bit_edges.h │ ├── bit_operation.h │ ├── contig_builder.h │ ├── contig_graph.cpp │ ├── contig_graph.h │ ├── contig_graph_branch_group.cpp │ ├── contig_graph_branch_group.h │ ├── contig_graph_path.h │ ├── contig_graph_vertex.h │ ├── contig_info.h │ ├── functional.h │ ├── hash.h │ ├── hash_graph.cpp │ ├── hash_graph.h │ ├── hash_graph_path.h │ ├── hash_graph_vertex.h │ ├── hash_table.h │ ├── kmer.h │ ├── pool.h │ ├── sequence.cpp │ ├── sequence.h │ └── vertex_status.h ├── iterate │ ├── contig_flank_index.h │ └── kmer_collector.h ├── kmlib │ ├── kmbit.h │ ├── kmbitvector.h │ ├── kmcompactvector.h │ ├── kmrns.h │ ├── kmsort.h │ ├── test_compactvector.cpp │ └── test_kmbit.cpp ├── localasm │ ├── hash_mapper.cpp │ ├── hash_mapper.h │ ├── local_assemble.cpp │ ├── local_assemble.h │ └── mapping_result_collector.h ├── main.cpp ├── main_assemble.cpp ├── main_buildlib.cpp ├── main_iterate.cpp ├── main_local_assemble.cpp ├── main_sdbg_build.cpp ├── megahit ├── parallel_hashmap │ ├── meminfo.h │ ├── phmap.h │ ├── phmap_base.h │ ├── phmap_bits.h │ ├── phmap_config.h │ ├── phmap_fwd_decl.h │ └── phmap_utils.h ├── pprintpp │ ├── charlist.hpp │ ├── pprintpp.hpp │ ├── stl_symbols.hpp │ └── typelist.hpp ├── sdbg │ ├── sdbg.h │ ├── sdbg_def.h │ ├── sdbg_item.h │ ├── sdbg_meta.cpp │ ├── sdbg_meta.h │ ├── sdbg_raw_content.cpp │ ├── sdbg_raw_content.h │ ├── sdbg_writer.cpp │ └── sdbg_writer.h ├── sequence │ ├── copy_substr.h │ ├── io │ │ ├── async_sequence_reader.h │ │ ├── base_reader.h │ │ ├── binary_reader.h │ │ ├── contig │ │ │ ├── contig_reader.h │ │ │ └── contig_writer.h │ │ ├── edge │ │ │ ├── edge_io_meta.h │ │ │ ├── edge_reader.h │ │ │ └── edge_writer.h │ │ ├── fastx_reader.cpp │ │ ├── fastx_reader.h │ │ ├── kseq.h │ │ ├── paired_fastx_reader.cpp │ │ ├── paired_fastx_reader.h │ │ ├── sequence_lib.cpp │ │ └── sequence_lib.h │ ├── kmer.h │ ├── kmer_plus.h │ └── sequence_package.h ├── sorting │ ├── base_engine.cpp │ ├── base_engine.h │ ├── edge_counter.h │ ├── kmer_counter.cpp │ ├── kmer_counter.h │ ├── kmsort_selector.cpp │ ├── kmsort_selector.h │ ├── read_to_sdbg.h │ ├── read_to_sdbg_s1.cpp │ ├── read_to_sdbg_s2.cpp │ ├── seq_to_sdbg.cpp │ └── seq_to_sdbg.h ├── tools │ ├── contigs_to_fastg.cpp │ ├── filter_by_len.cpp │ └── read_stat.cpp ├── utils │ ├── atomic_wrapper.h │ ├── buffered_reader.h │ ├── cpu_dispatch.h │ ├── histgram.h │ ├── mutex.h │ ├── options_description.cpp │ ├── options_description.h │ └── utils.h └── xxhash │ ├── xxh3.h │ ├── xxhash.c │ ├── xxhash.h │ └── xxhsum.c └── test_data ├── empty.fa ├── generate_random_fasta.py ├── loop.fa ├── r1.il.fa.gz ├── r2.il.fa.bz2 ├── r3_1.fa ├── r3_2.fa ├── r4.fa └── ref.fa /.clang-format: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voutcn/megahit/HEAD/.clang-format -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voutcn/megahit/HEAD/.gitignore -------------------------------------------------------------------------------- /.travis.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/voutcn/megahit/HEAD/.travis.yml 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