├── CHANGELOG.md ├── README.md ├── contrib ├── README.md ├── download-verify.sh └── download.tsv ├── core ├── .gitignore ├── BUILD.md ├── CMakeLists.txt ├── DEPENDENCIES.md ├── USAGE.md ├── alignments-filter.cpp ├── binner.cpp ├── build.sh ├── cmake-modules │ ├── FindBoost.cmake │ └── FindSqlite3.cmake ├── config.doxygen ├── extra │ ├── alignments2blasttab │ └── map-alignments-prot-dna ├── includes-external │ ├── boost │ │ ├── timer.hpp │ │ └── timer │ │ │ ├── config.hpp │ │ │ └── timer.hpp │ ├── seqan │ │ ├── align.h │ │ ├── align │ │ │ ├── align_base.h │ │ │ ├── align_cols.h │ │ │ ├── align_config.h │ │ │ ├── align_interface_wrapper.h │ │ │ ├── align_iterator_base.h │ │ │ ├── align_metafunctions.h │ │ │ ├── align_traceback.h │ │ │ ├── aligned_sequence_concept.h │ │ │ ├── alignment_algorithm_tags.h │ │ │ ├── alignment_operations.h │ │ │ ├── dp_algorithm_impl.h │ │ │ ├── dp_align_simd_helper.h │ │ │ ├── dp_band.h │ │ │ ├── dp_cell.h │ │ │ ├── dp_cell_affine.h │ │ │ ├── dp_cell_dynamic.h │ │ │ ├── dp_cell_linear.h │ │ │ ├── dp_context.h │ │ │ ├── dp_formula.h │ │ │ ├── dp_formula_affine.h │ │ │ ├── dp_formula_dynamic.h │ │ │ ├── dp_formula_linear.h │ │ │ ├── dp_matrix.h │ │ │ ├── dp_matrix_navigator.h │ │ │ ├── dp_matrix_navigator_score_matrix.h │ │ │ ├── dp_matrix_navigator_score_matrix_sparse.h │ │ │ ├── dp_matrix_navigator_trace_matrix.h │ │ │ ├── dp_matrix_sparse.h │ │ │ ├── dp_meta_info.h │ │ │ ├── dp_profile.h │ │ │ ├── dp_scout.h │ │ │ ├── dp_scout_simd.h │ │ │ ├── dp_setup.h │ │ │ ├── dp_trace_segment.h │ │ │ ├── dp_traceback_adaptor.h │ │ │ ├── dp_traceback_impl.h │ │ │ ├── evaluate_alignment.h │ │ │ ├── fragment.h │ │ │ ├── gap_anchor.h │ │ │ ├── gapped_value_type.h │ │ │ ├── gaps_anchor.h │ │ │ ├── gaps_array.h │ │ │ ├── gaps_base.h │ │ │ ├── gaps_iterator_anchor.h │ │ │ ├── gaps_iterator_array.h │ │ │ ├── gaps_iterator_base.h │ │ │ ├── global_alignment_banded.h │ │ │ ├── global_alignment_hirschberg_impl.h │ │ │ ├── global_alignment_myers_hirschberg_impl.h │ │ │ ├── global_alignment_myers_impl.h │ │ │ ├── global_alignment_specialized.h │ │ │ ├── global_alignment_unbanded.h │ │ │ ├── local_alignment_banded.h │ │ │ ├── local_alignment_banded_waterman_eggert_impl.h │ │ │ ├── local_alignment_enumeration.h │ │ │ ├── local_alignment_enumeration_banded.h │ │ │ ├── local_alignment_enumeration_unbanded.h │ │ │ ├── local_alignment_unbanded.h │ │ │ ├── local_alignment_waterman_eggert_impl.h │ │ │ └── matrix_base.h │ │ ├── align_extend.h │ │ ├── align_extend │ │ │ ├── align_extend.h │ │ │ ├── align_extend_base.h │ │ │ └── dp_scout_xdrop.h │ │ ├── align_parallel.h │ │ ├── align_parallel │ │ │ ├── async_wave_execution_interface.h │ │ │ ├── dp_kernel_adaptor.h │ │ │ ├── dp_parallel_execution_policies.h │ │ │ ├── dp_parallel_scout.h │ │ │ ├── dp_parallel_scout_simd.h │ │ │ ├── dp_settings.h │ │ │ ├── dp_traits.h │ │ │ ├── parallel_align_interface.h │ │ │ ├── wavefront_alignment_executor.h │ │ │ ├── wavefront_alignment_result.h │ │ │ ├── wavefront_alignment_scheduler.h │ │ │ ├── wavefront_alignment_task.h │ │ │ ├── wavefront_alignment_thread_local_storage.h │ │ │ ├── wavefront_task.h │ │ │ ├── wavefront_task_event.h │ │ │ ├── wavefront_task_executor.h │ │ │ ├── wavefront_task_queue.h │ │ │ ├── wavefront_task_scheduler.h │ │ │ └── wavefront_task_util.h │ │ ├── align_profile.h │ │ ├── align_profile │ │ │ ├── add_to_profile.h │ │ │ └── score_profile_seq.h │ │ ├── align_split.h │ │ ├── align_split │ │ │ ├── align_split_interface.h │ │ │ └── dp_scout_split.h │ │ ├── alignment_free.h │ │ ├── alignment_free │ │ │ ├── af_d2.h │ │ │ ├── af_d2star.h │ │ │ ├── af_d2z.h │ │ │ ├── af_n2.h │ │ │ ├── alignment_free_base.h │ │ │ ├── alignment_free_comparison.h │ │ │ └── kmer_functions.h │ │ ├── arg_parse.h │ │ ├── arg_parse │ │ │ ├── arg_parse_argument.h │ │ │ ├── arg_parse_ctd_support.h │ │ │ ├── arg_parse_doc.h │ │ │ ├── arg_parse_exceptions.h │ │ │ ├── arg_parse_option.h │ │ │ ├── arg_parse_parse.h │ │ │ ├── arg_parse_type_support.h │ │ │ ├── arg_parse_version_check.h │ │ │ ├── argument_parser.h │ │ │ ├── tool_doc.h │ │ │ └── xml_support.h │ │ ├── bam_io.h │ │ ├── bam_io │ │ │ ├── bam_alignment_record.h │ │ │ ├── bam_alignment_record_util.h │ │ │ ├── bam_file.h │ │ │ ├── bam_header_record.h │ │ │ ├── bam_index_bai.h │ │ │ ├── bam_io_context.h │ │ │ ├── bam_sam_conversion.h │ │ │ ├── bam_scanner_cache.h │ │ │ ├── bam_tags_dict.h │ │ │ ├── cigar.h │ │ │ ├── read_bam.h │ │ │ ├── read_sam.h │ │ │ ├── write_bam.h │ │ │ └── write_sam.h │ │ ├── basic.h │ │ ├── basic │ │ │ ├── aggregate_concept.h │ │ │ ├── allocator_chunkpool.h │ │ │ ├── allocator_interface.h │ │ │ ├── allocator_multipool.h │ │ │ ├── allocator_simple.h │ │ │ ├── allocator_singlepool.h │ │ │ ├── allocator_to_std.h │ │ │ ├── alphabet_adapt_builtins.h │ │ │ ├── alphabet_bio.h │ │ │ ├── alphabet_concept.h │ │ │ ├── alphabet_math.h │ │ │ ├── alphabet_profile.h │ │ │ ├── alphabet_qualities.h │ │ │ ├── alphabet_residue.h │ │ │ ├── alphabet_residue_funcs.h │ │ │ ├── alphabet_residue_tabs.h │ │ │ ├── alphabet_simple_type.h │ │ │ ├── alphabet_storage.h │ │ │ ├── array_construct_destruct.h │ │ │ ├── basic_aggregate.h │ │ │ ├── basic_allocator.h │ │ │ ├── basic_alphabet.h │ │ │ ├── basic_concept.h │ │ │ ├── basic_container.h │ │ │ ├── basic_debug.h │ │ │ ├── basic_device.h │ │ │ ├── basic_exception.h │ │ │ ├── basic_functors.h │ │ │ ├── basic_fundamental.h │ │ │ ├── basic_iterator.h │ │ │ ├── basic_math.h │ │ │ ├── basic_metaprogramming.h │ │ │ ├── basic_parallelism.h │ │ │ ├── basic_proxy.h │ │ │ ├── basic_smart_pointer.h │ │ │ ├── basic_stream.h │ │ │ ├── basic_tangle.h │ │ │ ├── basic_type.h │ │ │ ├── basic_view.h │ │ │ ├── boost_preprocessor_subset.h │ │ │ ├── builtin_functions.h │ │ │ ├── concept_checking.h │ │ │ ├── container_concept.h │ │ │ ├── debug_helper.h │ │ │ ├── debug_test_system.h │ │ │ ├── fundamental_chunking.h │ │ │ ├── fundamental_comparison.h │ │ │ ├── fundamental_concepts.h │ │ │ ├── fundamental_conversion.h │ │ │ ├── fundamental_metafunctions.h │ │ │ ├── fundamental_tags.h │ │ │ ├── fundamental_transport.h │ │ │ ├── holder_base.h │ │ │ ├── holder_simple.h │ │ │ ├── holder_tristate.h │ │ │ ├── hosted_type_interface.h │ │ │ ├── iterator_adapt_pointer.h │ │ │ ├── iterator_adapt_std.h │ │ │ ├── iterator_adaptor.h │ │ │ ├── iterator_base.h │ │ │ ├── iterator_concept.h │ │ │ ├── iterator_counting.h │ │ │ ├── iterator_interface.h │ │ │ ├── iterator_position.h │ │ │ ├── iterator_range.h │ │ │ ├── iterator_zip.h │ │ │ ├── macro_deprecated.h │ │ │ ├── math_functions.h │ │ │ ├── math_log_space_value.h │ │ │ ├── metaprogramming_control.h │ │ │ ├── metaprogramming_enable_if.h │ │ │ ├── metaprogramming_logic.h │ │ │ ├── metaprogramming_math.h │ │ │ ├── metaprogramming_type.h │ │ │ ├── metaprogramming_type_algebra.h │ │ │ ├── pair_base.h │ │ │ ├── pair_bit_compressed.h │ │ │ ├── pair_packed.h │ │ │ ├── profiling.h │ │ │ ├── property_map_concept.h │ │ │ ├── proxy_base.h │ │ │ ├── proxy_iterator.h │ │ │ ├── test_system.h │ │ │ ├── triple_base.h │ │ │ ├── triple_packed.h │ │ │ ├── tuple_base.h │ │ │ ├── tuple_bit_compressed.h │ │ │ └── volatile_ptr.h │ │ ├── bed_io.h │ │ ├── bed_io │ │ │ ├── bed_file.h │ │ │ ├── bed_record.h │ │ │ ├── read_bed.h │ │ │ └── write_bed.h │ │ ├── blast.h │ │ ├── blast │ │ │ ├── blast_base.h │ │ │ ├── blast_io_context.h │ │ │ ├── blast_record.h │ │ │ ├── blast_report_out.h │ │ │ ├── blast_statistics.h │ │ │ ├── blast_tabular.h │ │ │ ├── blast_tabular_in.h │ │ │ ├── blast_tabular_lowlevel.h │ │ │ └── blast_tabular_out.h │ │ ├── consensus.h │ │ ├── consensus │ │ │ ├── consensus_aligner.h │ │ │ ├── consensus_aligner_interface.h │ │ │ ├── consensus_alignment_options.h │ │ │ ├── consensus_base.h │ │ │ ├── consensus_builder.h │ │ │ ├── consensus_library.h │ │ │ ├── consensus_realign.h │ │ │ ├── consensus_score.h │ │ │ ├── overlap_info_computation.h │ │ │ └── overlapper.h │ │ ├── file.h │ │ ├── file │ │ │ ├── file_base.h │ │ │ ├── file_cstyle.h │ │ │ ├── file_forwards.h │ │ │ ├── file_interface.h │ │ │ ├── file_mapping.h │ │ │ ├── file_page.h │ │ │ ├── string_external.h │ │ │ └── string_mmap.h │ │ ├── find.h │ │ ├── find │ │ │ ├── find_abndm.h │ │ │ ├── find_ahocorasick.h │ │ │ ├── find_base.h │ │ │ ├── find_begin.h │ │ │ ├── find_bndm.h │ │ │ ├── find_bom.h │ │ │ ├── find_hamming_simple.h │ │ │ ├── find_horspool.h │ │ │ ├── find_lambda.h │ │ │ ├── find_multi.h │ │ │ ├── find_multiple_bfam.h │ │ │ ├── find_multiple_shiftand.h │ │ │ ├── find_myers_ukkonen.h │ │ │ ├── find_pattern_base.h │ │ │ ├── find_pex.h │ │ │ ├── find_score.h │ │ │ ├── find_set_horspool.h │ │ │ ├── find_shiftand.h │ │ │ ├── find_shiftor.h │ │ │ ├── find_simple.h │ │ │ ├── find_wild_shiftand.h │ │ │ └── find_wumanber.h │ │ ├── gff_io.h │ │ ├── gff_io │ │ │ ├── gff_file.h │ │ │ └── gff_io_base.h │ │ ├── graph_algorithms.h │ │ ├── graph_algorithms │ │ │ ├── all_pairs_shortest_path.h │ │ │ ├── bellman_ford.h │ │ │ ├── bipartite_matching.h │ │ │ ├── breadth_first_search.h │ │ │ ├── connected_components.h │ │ │ ├── depth_first_search.h │ │ │ ├── dijkstra.h │ │ │ ├── floyd_warshall.h │ │ │ ├── ford_fulkerson.h │ │ │ ├── graph_algorithm_heap_tree.h │ │ │ ├── graph_algorithm_hmm.h │ │ │ ├── graph_algorithm_lis_his.h │ │ │ ├── kruskal.h │ │ │ ├── maximum_weighted_matching.h │ │ │ ├── path_growing.h │ │ │ ├── prim.h │ │ │ ├── single_source_shortest_path.h │ │ │ ├── strongly_connected_compnents.h │ │ │ ├── topological_sort.h │ │ │ ├── transitive_closure.h │ │ │ ├── weakly_connected_components.h │ │ │ └── weighted_bipartite_matching.h │ │ ├── graph_align.h │ │ ├── graph_align │ │ │ ├── graph_algorithm_refine_align.h │ │ │ ├── graph_algorithm_refine_aligngraph.h │ │ │ ├── graph_algorithm_refine_annotation.h │ │ │ ├── graph_algorithm_refine_exact.h │ │ │ ├── graph_algorithm_refine_exact_iterative.h │ │ │ ├── graph_algorithm_refine_fragment.h │ │ │ ├── graph_algorithm_refine_inexact.h │ │ │ ├── graph_algorithm_refine_scoring.h │ │ │ ├── graph_impl_align.h │ │ │ └── graph_impl_align_adapt.h │ │ ├── graph_msa.h │ │ ├── graph_msa │ │ │ ├── graph_align_tcoffee_base.h │ │ │ ├── graph_align_tcoffee_distance.h │ │ │ ├── graph_align_tcoffee_guidetree.h │ │ │ ├── graph_align_tcoffee_io.h │ │ │ ├── graph_align_tcoffee_kmer.h │ │ │ ├── graph_align_tcoffee_library.h │ │ │ ├── graph_align_tcoffee_msa.h │ │ │ ├── graph_align_tcoffee_progressive.h │ │ │ └── graph_align_tcoffee_refinement.h │ │ ├── graph_types.h │ │ ├── graph_types │ │ │ ├── graph_base.h │ │ │ ├── graph_drawing.h │ │ │ ├── graph_edgestump.h │ │ │ ├── graph_idmanager.h │ │ │ ├── graph_impl_automaton.h │ │ │ ├── graph_impl_directed.h │ │ │ ├── graph_impl_hmm.h │ │ │ ├── graph_impl_oracle.h │ │ │ ├── graph_impl_tree.h │ │ │ ├── graph_impl_trie.h │ │ │ ├── graph_impl_undirected.h │ │ │ ├── graph_impl_wordgraph.h │ │ │ ├── graph_interface.h │ │ │ ├── graph_iterator.h │ │ │ ├── graph_iterator_adjacency.h │ │ │ ├── graph_iterator_bfs.h │ │ │ ├── graph_iterator_dfs.h │ │ │ ├── graph_iterator_edge.h │ │ │ ├── graph_iterator_outedge.h │ │ │ ├── graph_iterator_vertex.h │ │ │ ├── graph_utility_parsing.h │ │ │ ├── property_map_generic.h │ │ │ ├── property_map_internal.h │ │ │ └── property_map_internal_pointer.h │ │ ├── index.h │ │ ├── index │ │ │ ├── find2_backtracking.h │ │ │ ├── find2_base.h │ │ │ ├── find2_functors.h │ │ │ ├── find2_index.h │ │ │ ├── find2_index_approx.h │ │ │ ├── find2_index_multi.h │ │ │ ├── find2_vstree_factory.h │ │ │ ├── find_backtracking.h │ │ │ ├── find_index.h │ │ │ ├── find_index_approx.h │ │ │ ├── find_index_binary.h │ │ │ ├── find_index_esa.h │ │ │ ├── find_index_lambda.h │ │ │ ├── find_index_qgram.h │ │ │ ├── find_pigeonhole.h │ │ │ ├── find_quasar.h │ │ │ ├── find_swift.h │ │ │ ├── index_base.h │ │ │ ├── index_bidirectional.h │ │ │ ├── index_bidirectional_stree.h │ │ │ ├── index_bifm.h │ │ │ ├── index_bifm_stree.h │ │ │ ├── index_bwt.h │ │ │ ├── index_childtab.h │ │ │ ├── index_device.h │ │ │ ├── index_dfi.h │ │ │ ├── index_esa_algs.h │ │ │ ├── index_esa_algs_multi.h │ │ │ ├── index_esa_base.h │ │ │ ├── index_esa_drawing.h │ │ │ ├── index_esa_stree.h │ │ │ ├── index_fm.h │ │ │ ├── index_fm_compressed_sa.h │ │ │ ├── index_fm_compressed_sa_iterator.h │ │ │ ├── index_fm_dox.h │ │ │ ├── index_fm_lf_table.h │ │ │ ├── index_fm_rank_dictionary_base.h │ │ │ ├── index_fm_rank_dictionary_levels.h │ │ │ ├── index_fm_rank_dictionary_naive.h │ │ │ ├── index_fm_rank_dictionary_wt.h │ │ │ ├── index_fm_right_array_binary_tree.h │ │ │ ├── index_fm_right_array_binary_tree_iterator.h │ │ │ ├── index_fm_sparse_string.h │ │ │ ├── index_fm_stree.h │ │ │ ├── index_forwards.h │ │ │ ├── index_lcp.h │ │ │ ├── index_lcp_tree.h │ │ │ ├── index_pizzachili.h │ │ │ ├── index_pizzachili_find.h │ │ │ ├── index_pizzachili_string.h │ │ │ ├── index_qgram.h │ │ │ ├── index_qgram_bucketrefinement.h │ │ │ ├── index_qgram_openaddressing.h │ │ │ ├── index_qgram_stree.h │ │ │ ├── index_sa_btree.h │ │ │ ├── index_sa_bwtwalk.h │ │ │ ├── index_sa_lss.h │ │ │ ├── index_sa_mm.h │ │ │ ├── index_sa_qsort.h │ │ │ ├── index_sa_stree.h │ │ │ ├── index_sa_truncated.h │ │ │ ├── index_shawarma.h │ │ │ ├── index_shims.h │ │ │ ├── index_skew3.h │ │ │ ├── index_skew7.h │ │ │ ├── index_skew7_multi.h │ │ │ ├── index_view.h │ │ │ ├── index_wotd.h │ │ │ ├── pipe_merger3.h │ │ │ ├── pipe_merger7.h │ │ │ ├── pizzachili_api.h │ │ │ ├── pump_extender3.h │ │ │ ├── pump_extender7.h │ │ │ ├── pump_lcp_core.h │ │ │ ├── pump_separator7.h │ │ │ ├── radix.h │ │ │ ├── repeat_base.h │ │ │ ├── shape_base.h │ │ │ ├── shape_gapped.h │ │ │ ├── shape_minimizer.h │ │ │ ├── shape_onegapped.h │ │ │ ├── shape_predefined.h │ │ │ └── shape_threshold.h │ │ ├── journaled_set.h │ │ ├── journaled_set │ │ │ ├── journal_alignment_interface.h │ │ │ ├── journal_alignment_traceback_adaptor.h │ │ │ ├── journaled_set_base.h │ │ │ ├── journaled_set_impl.h │ │ │ ├── journaled_set_join.h │ │ │ ├── journaled_set_join_config.h │ │ │ ├── journaled_set_join_global_align_compact.h │ │ │ ├── journaled_set_join_global_align_manhatten.h │ │ │ ├── journaled_set_journal_trace_descriptor.h │ │ │ └── score_biaffine.h │ │ ├── journaled_string_tree.h │ │ ├── journaled_string_tree │ │ │ ├── delta_map.h │ │ │ ├── delta_map_entry.h │ │ │ ├── delta_map_iterator.h │ │ │ ├── delta_store.h │ │ │ ├── journaled_string_tree_base.h │ │ │ ├── journaled_string_tree_impl.h │ │ │ ├── journaled_string_tree_sequence_buffer.h │ │ │ ├── journaled_string_tree_traverser.h │ │ │ ├── journaled_string_tree_traverser_node.h │ │ │ ├── journaled_string_tree_traverser_util.h │ │ │ ├── jst_extension_base.h │ │ │ ├── jst_extension_horspool.h │ │ │ ├── jst_extension_myers_ukkonen.h │ │ │ ├── jst_extension_shiftand.h │ │ │ ├── jst_extension_shiftor.h │ │ │ ├── observable.h │ │ │ └── stack_observer.h │ │ ├── map.h │ │ ├── map │ │ │ ├── map_adapter_stl.h │ │ │ ├── map_base.h │ │ │ ├── map_chooser.h │ │ │ ├── map_skiplist.h │ │ │ ├── map_vector.h │ │ │ ├── sumlist.h │ │ │ ├── sumlist_mini.h │ │ │ └── sumlist_skip.h │ │ ├── math.h │ │ ├── math │ │ │ ├── math_common_factor.h │ │ │ ├── math_operators.h │ │ │ └── math_rational.h │ │ ├── misc │ │ │ ├── accumulators.h │ │ │ ├── base.h │ │ │ ├── bit_twiddling.h │ │ │ ├── bit_twiddling_functors.h │ │ │ ├── dequeue.h │ │ │ ├── edit_environment.h │ │ │ ├── interval_tree.h │ │ │ ├── map.h │ │ │ ├── memset.h │ │ │ ├── name_store_cache.h │ │ │ ├── priority_type_base.h │ │ │ ├── priority_type_heap.h │ │ │ ├── set.h │ │ │ ├── svg.h │ │ │ ├── terminal.h │ │ │ └── union_find.h │ │ ├── modifier.h │ │ ├── modifier │ │ │ ├── cyclic_shape.h │ │ │ ├── modifier_alphabet.h │ │ │ ├── modifier_alphabet_expansion.h │ │ │ ├── modifier_cyclic_shape.h │ │ │ ├── modifier_functors.h │ │ │ ├── modifier_iterator.h │ │ │ ├── modifier_padding.h │ │ │ ├── modifier_position.h │ │ │ ├── modifier_reverse.h │ │ │ ├── modifier_shortcuts.h │ │ │ ├── modifier_string.h │ │ │ └── modifier_view.h │ │ ├── parallel.h │ │ ├── parallel │ │ │ ├── enumerable_thread_local.h │ │ │ ├── enumerable_thread_local_iterator.h │ │ │ ├── parallel_algorithms.h │ │ │ ├── parallel_atomic_misc.h │ │ │ ├── parallel_atomic_primitives.h │ │ │ ├── parallel_lock.h │ │ │ ├── parallel_macros.h │ │ │ ├── parallel_queue.h │ │ │ ├── parallel_queue_suspendable.h │ │ │ ├── parallel_resource_pool.h │ │ │ ├── parallel_sequence.h │ │ │ ├── parallel_serializer.h │ │ │ ├── parallel_splitting.h │ │ │ ├── parallel_tags.h │ │ │ └── parallel_thread_pool.h │ │ ├── parse_lm.h │ │ ├── parse_lm │ │ │ ├── local_match_store.h │ │ │ ├── parse_blastn_tabular.h │ │ │ ├── parse_lastz_general.h │ │ │ └── parse_stellar_gff.h │ │ ├── pipe.h │ │ ├── pipe │ │ │ ├── pipe_base.h │ │ │ ├── pipe_caster.h │ │ │ ├── pipe_counter.h │ │ │ ├── pipe_echoer.h │ │ │ ├── pipe_edit_environment.h │ │ │ ├── pipe_filter.h │ │ │ ├── pipe_iterator.h │ │ │ ├── pipe_joiner.h │ │ │ ├── pipe_namer.h │ │ │ ├── pipe_sampler.h │ │ │ ├── pipe_shifter.h │ │ │ ├── pipe_source.h │ │ │ ├── pipe_tupler.h │ │ │ ├── pool_base.h │ │ │ ├── pool_mapper.h │ │ │ └── pool_sorter.h │ │ ├── platform.h │ │ ├── random.h │ │ ├── random │ │ │ ├── random_base.h │ │ │ ├── random_beta.h │ │ │ └── random_util.h │ │ ├── realign.h │ │ ├── realign │ │ │ ├── realign_base.h │ │ │ └── realign_helper_functions.h │ │ ├── reduced_aminoacid.h │ │ ├── reduced_aminoacid │ │ │ ├── reduced_aminoacid_base.h │ │ │ ├── reduced_aminoacid_base_late.h │ │ │ ├── reduced_aminoacid_buchfink11_base.h │ │ │ ├── reduced_aminoacid_buchfink11_tables.h │ │ │ ├── reduced_aminoacid_cannata10_base.h │ │ │ ├── reduced_aminoacid_cannata10_tables.h │ │ │ ├── reduced_aminoacid_cluster_red_base.h │ │ │ ├── reduced_aminoacid_cluster_red_tables_20_to_n_b62.h │ │ │ ├── reduced_aminoacid_cluster_red_tables_22_to_n_b62.h │ │ │ ├── reduced_aminoacid_cluster_red_tables_24_to_n_b62.h │ │ │ ├── reduced_aminoacid_li10_base.h │ │ │ ├── reduced_aminoacid_li10_tables.h │ │ │ ├── reduced_aminoacid_murphy10_base.h │ │ │ ├── reduced_aminoacid_murphy10_tables.h │ │ │ ├── reduced_aminoacid_murphy5_base.h │ │ │ ├── reduced_aminoacid_murphy5_tables.h │ │ │ ├── reduced_aminoacid_solis10_base.h │ │ │ └── reduced_aminoacid_solis10_tables.h │ │ ├── rna_io.h │ │ ├── rna_io │ │ │ ├── bpseq_read_write.h │ │ │ ├── connect_read_write.h │ │ │ ├── dot_bracket_read_write.h │ │ │ ├── ebpseq_read_write.h │ │ │ ├── rna_header.h │ │ │ ├── rna_io_context.h │ │ │ ├── rna_record.h │ │ │ ├── rna_struct_file.h │ │ │ ├── stockholm_read_write.h │ │ │ └── vienna_read_write.h │ │ ├── roi_io.h │ │ ├── roi_io │ │ │ ├── read_roi.h │ │ │ ├── roi_file.h │ │ │ ├── roi_io_context.h │ │ │ ├── roi_record.h │ │ │ └── write_roi.h │ │ ├── score.h │ │ ├── score │ │ │ ├── score_base.h │ │ │ ├── score_edit.h │ │ │ ├── score_matrix.h │ │ │ ├── score_matrix_data.h │ │ │ ├── score_matrix_dyn.h │ │ │ ├── score_matrix_io.h │ │ │ ├── score_simd_wrapper.h │ │ │ └── score_simple.h │ │ ├── seeds.h │ │ ├── seeds │ │ │ ├── banded_chain_alignment.h │ │ │ ├── banded_chain_alignment_impl.h │ │ │ ├── banded_chain_alignment_profile.h │ │ │ ├── banded_chain_alignment_scout.h │ │ │ ├── banded_chain_alignment_traceback.h │ │ │ ├── basic_iter_indirect.h │ │ │ ├── seeds_base.h │ │ │ ├── seeds_combination.h │ │ │ ├── seeds_extension.h │ │ │ ├── seeds_global_chaining.h │ │ │ ├── seeds_global_chaining_base.h │ │ │ ├── seeds_global_chaining_gusfield.h │ │ │ ├── seeds_seed_base.h │ │ │ ├── seeds_seed_chained.h │ │ │ ├── seeds_seed_diagonal.h │ │ │ ├── seeds_seed_set_base.h │ │ │ ├── seeds_seed_set_non_scored.h │ │ │ ├── seeds_seed_set_scored.h │ │ │ ├── seeds_seed_set_unordered.h │ │ │ └── seeds_seed_simple.h │ │ ├── seq_io.h │ │ ├── seq_io │ │ │ ├── bam_sam.h │ │ │ ├── fai_index.h │ │ │ ├── fasta_fastq.h │ │ │ ├── genomic_region.h │ │ │ ├── read_embl.h │ │ │ ├── read_genbank.h │ │ │ └── sequence_file.h │ │ ├── sequence.h │ │ ├── sequence │ │ │ ├── adapt_array_pointer.h │ │ │ ├── adapt_stl_container.h │ │ │ ├── container_view.h │ │ │ ├── container_view_zip.h │ │ │ ├── iter_concat_virtual.h │ │ │ ├── segment_base.h │ │ │ ├── segment_infix.h │ │ │ ├── segment_prefix.h │ │ │ ├── segment_suffix.h │ │ │ ├── segment_utils.h │ │ │ ├── sequence_concatenator.h │ │ │ ├── sequence_forwards.h │ │ │ ├── sequence_interface.h │ │ │ ├── sequence_lexical.h │ │ │ ├── sequence_shortcuts.h │ │ │ ├── string_alloc.h │ │ │ ├── string_array.h │ │ │ ├── string_base.h │ │ │ ├── string_block.h │ │ │ ├── string_cstyle.h │ │ │ ├── string_packed.h │ │ │ ├── string_packed_old.h │ │ │ ├── string_set_base.h │ │ │ ├── string_set_concat_direct.h │ │ │ ├── string_set_dependent_generous.h │ │ │ ├── string_set_dependent_tight.h │ │ │ ├── string_set_owner.h │ │ │ ├── string_set_segment.h │ │ │ └── string_set_view.h │ │ ├── sequence_journaled.h │ │ ├── sequence_journaled │ │ │ ├── journal_entries_sorted_array.h │ │ │ ├── journal_entry.h │ │ │ ├── sequence_journaled.h │ │ │ ├── sequence_journaled_iterator.h │ │ │ └── sequence_journaled_iterator_fast.h │ │ ├── simd.h │ │ ├── simd │ │ │ ├── simd_base.h │ │ │ ├── simd_base_seqan_impl.h │ │ │ ├── simd_base_seqan_impl_avx2.h │ │ │ ├── simd_base_seqan_impl_avx512.h │ │ │ ├── simd_base_seqan_impl_sse4.2.h │ │ │ ├── simd_base_seqan_interface.h │ │ │ └── simd_base_umesimd_impl.h │ │ ├── simple_intervals_io.h │ │ ├── simple_intervals_io │ │ │ ├── simple_intervals_file.h │ │ │ └── simple_intervals_io.h │ │ ├── statistics.h │ │ ├── statistics │ │ │ ├── statistics_base.h │ │ │ └── statistics_markov_model.h │ │ ├── store.h │ │ ├── store │ │ │ ├── store_align.h │ │ │ ├── store_align_intervals.h │ │ │ ├── store_all.h │ │ │ ├── store_annotation.h │ │ │ ├── store_base.h │ │ │ ├── store_contig.h │ │ │ ├── store_intervaltree.h │ │ │ ├── store_io.h │ │ │ ├── store_io_gff.h │ │ │ ├── store_io_sam.h │ │ │ ├── store_io_ucsc.h │ │ │ ├── store_library.h │ │ │ ├── store_matepair.h │ │ │ └── store_read.h │ │ ├── stream.h │ │ ├── stream │ │ │ ├── adapt_ios.h │ │ │ ├── buffered_stream.h │ │ │ ├── file_stream.h │ │ │ ├── formatted_file.h │ │ │ ├── guess_format.h │ │ │ ├── iostream_bgzf.h │ │ │ ├── iostream_bzip2.h │ │ │ ├── iostream_bzip2_impl.h │ │ │ ├── iostream_zip.h │ │ │ ├── iostream_zip_impl.h │ │ │ ├── iostream_zutil.h │ │ │ ├── iter_stream.h │ │ │ ├── lexical_cast.h │ │ │ ├── stream_base.h │ │ │ ├── stream_compressor.h │ │ │ ├── tokenization.h │ │ │ └── virtual_stream.h │ │ ├── system.h │ │ ├── system │ │ │ ├── file_async.h │ │ │ ├── file_directory.h │ │ │ ├── file_forwards.h │ │ │ ├── file_sync.h │ │ │ ├── system_base.h │ │ │ ├── system_event_win.h │ │ │ └── system_forwards.h │ │ ├── tabix_io.h │ │ ├── tabix_io │ │ │ └── tabix_index_tbi.h │ │ ├── translation.h │ │ ├── translation │ │ │ ├── translation.h │ │ │ └── translation_tables.h │ │ ├── ucsc_io.h │ │ ├── ucsc_io │ │ │ ├── ucsc_file.h │ │ │ ├── ucsc_io.h │ │ │ └── ucsc_record.h │ │ ├── vcf_io.h │ │ ├── vcf_io │ │ │ ├── read_vcf.h │ │ │ ├── vcf_file.h │ │ │ ├── vcf_header.h │ │ │ ├── vcf_header_record.h │ │ │ ├── vcf_io_context.h │ │ │ ├── vcf_record.h │ │ │ └── write_vcf.h │ │ └── version.h │ ├── tree.hh │ ├── tsl │ │ ├── array-hash │ │ │ ├── array_growth_policy.h │ │ │ ├── array_hash.h │ │ │ ├── array_map.h │ │ │ └── array_set.h │ │ ├── htrie_hash.h │ │ ├── htrie_map.h │ │ └── htrie_set.h │ └── zstr │ │ ├── strict_fstream.hh │ │ └── zstr.hh ├── src │ ├── accessconv.cpp │ ├── accessconv.hh │ ├── alignmentrecord.cpp │ ├── alignmentrecord.hh │ ├── alignmentsfilter.hh │ ├── bioboxes.cpp │ ├── bioboxes.hh │ ├── boundedbuffer.hh │ ├── concurrentoutstream.hh │ ├── constants.hh │ ├── exception.hh │ ├── faidx.h │ ├── fastnodemap.hh │ ├── fileparser.hh │ ├── ncbidata.cpp │ ├── ncbidata.hh │ ├── ostreamtwrapperts.hh │ ├── predictionranges.hh │ ├── predictionrecord.cpp │ ├── predictionrecord.hh │ ├── predictionrecordbinning.hh │ ├── profiling.hh │ ├── sequencestorage.hh │ ├── sqlite3pp.cpp │ ├── sqlite3pp.hh │ ├── taxonfilter.hh │ ├── taxonomyinterface.cpp │ ├── taxonomyinterface.hh │ ├── taxonpredictionmodel.hh │ ├── taxonpredictionmodelsequence.hh │ ├── taxontree.cpp │ ├── taxontree.hh │ ├── tree.hh │ ├── types.hh │ └── utils.hh ├── taxator.cpp ├── taxknife.cpp └── unittest_ncbitaxonomy.cpp ├── doc └── fileformats.md ├── extended ├── .gitignore ├── DEPENDENCIES.md ├── README.md ├── bin │ ├── alignments-filter │ ├── binner │ ├── blastn │ ├── blastp │ ├── fasta-strip-identifier │ ├── ktImportText │ ├── last-merge-batches │ ├── last_maf_convert.py │ ├── lastal │ ├── lastal-parallel │ ├── lastdb │ ├── lastmaf2alignments │ ├── lastmaf2alignments-parallel │ ├── lz4 │ ├── makeblastdb │ ├── orfm │ ├── parallel │ ├── taxator │ ├── taxatortk.py │ ├── taxknife │ └── taxsummary2krona ├── binning-blast-protein.bash ├── binning-blast.bash ├── binning-last.bash ├── index-blast-protein.bash ├── index-blast.bash ├── index-last.bash ├── lib │ ├── KronaTools.pm │ ├── common.sh │ └── krona │ │ ├── favicon.uri │ │ ├── hidden.uri │ │ ├── krona-2.0.js │ │ ├── loading.uri │ │ ├── logo-med.uri │ │ ├── logo-small.uri │ │ 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