├── .gitignore ├── LICENSE ├── Makefile ├── README.md ├── astyle.txt ├── bamhash_checksum_bam.cpp ├── bamhash_checksum_common.cpp ├── bamhash_checksum_common.h ├── bamhash_checksum_fasta.cpp ├── bamhash_checksum_fastq.cpp ├── seqan ├── LICENSE ├── align.h ├── align │ ├── align_base.h │ ├── align_cols.h │ ├── align_config.h │ ├── align_iterator_base.h │ ├── align_metafunctions.h │ ├── align_traceback.h │ ├── alignment_algorithm_tags.h │ ├── alignment_operations.h │ ├── dp_algorithm_impl.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_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_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 │ ├── 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_simd_vector.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 │ ├── 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 │ ├── 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 ├── hts_io.h ├── hts_io │ ├── bam_alignment_record.h │ ├── hts_alignment_record.h │ ├── hts_alignment_record_utils.h │ └── hts_file.h ├── index.h ├── index │ ├── find2_backtracking.h │ ├── find2_base.h │ ├── find2_functors.h │ ├── find2_index.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_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_device.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 │ └── observable.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 │ ├── cuda.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_position.h │ ├── modifier_reverse.h │ ├── modifier_shortcuts.h │ ├── modifier_string.h │ └── modifier_view.h ├── parallel.h ├── parallel │ ├── 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 ├── 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 ├── platform │ ├── platform_gcc.h │ ├── platform_icc.h │ ├── platform_mingw.h │ ├── platform_nvcc.h │ ├── platform_pgi.h │ ├── platform_solaris.h │ ├── platform_windows.h │ └── windows_stdint.h ├── random.h ├── random │ ├── ext_MersenneTwister.h │ ├── random_base.h │ ├── random_beta.h │ ├── random_beta_kfunc.h │ ├── random_geometric.h │ ├── random_lognormal.h │ ├── random_mt19937.h │ ├── random_normal.h │ ├── random_rng_functor.h │ ├── random_shuffle.h │ └── random_uniform.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_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_murphy10_base.h │ └── reduced_aminoacid_murphy10_tables.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_io.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 │ ├── 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 │ ├── adapt_thrust_vector.h │ ├── container_view.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_device.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 ├── simple_intervals_io.h ├── simple_intervals_io │ ├── simple_intervals_file.h │ └── simple_intervals_io.h ├── statistics.h ├── statistics │ ├── .statistics_markov_model.h.swp │ ├── 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_condition.h │ ├── system_critical_section.h │ ├── system_event.h │ ├── system_forwards.h │ ├── system_mutex.h │ └── system_thread.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 │ ├── tabix.h │ ├── vcf_file.h │ ├── vcf_header.h │ ├── vcf_header_record.h │ ├── vcf_io_context.h │ ├── vcf_record.h │ └── write_vcf.h └── version.h └── test └── Makefile /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DecodeGenetics/BamHash/HEAD/.gitignore -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DecodeGenetics/BamHash/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/DecodeGenetics/BamHash/HEAD/Makefile -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- 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