seqan/2.4.0

SeqAn is an open source C++ library of efficient algorithms and data structures for the analysis of sequences with the focus on biological data. Our library applies a unique generic design that guarantees high performance, generality, extensibility, and integration with other libraries. SeqAn is easy to use and simplifies the development of new software tools with a minimal loss of performance.
Recipe info
2023-07-18

Available packages
Header Only

Install
Add the following line to your conanfile.txt:
[requires]
seqan/2.4.0

Using seqan

Note

If you are new with Conan, we recommend to read the section how to consume packages.

If you need additional assistance, please ask a question in the Conan Center Index repository.

Simplest use case consuming this recipe and assuming CMake as your local build tool:

[requires]
seqan/2.4.0
[generators]
CMakeDeps
CMakeToolchain
[layout]
cmake_layout
from conan import ConanFile
from conan.tools.cmake import cmake_layout


class ExampleRecipe(ConanFile):
    settings = "os", "compiler", "build_type", "arch"
    generators = "CMakeDeps", "CMakeToolchain"

    def requirements(self):
        self.requires("seqan/2.4.0")

    def layout(self):
        cmake_layout(self)

Now, you can run this Conan command to locally install (and build if necessary) this recipe and its dependencies (if any):

$ conan install conanfile.txt --build=missing

Useful information to take into account to consume this library:


These are the main declared targets:

  • CMake package name(s): seqan
  • CMake target name(s): seqan::seqan
  • pkg-config file name(s): seqan.pc

A simple use case using the CMake file name and the global target:

# ...
find_package(seqan REQUIRED)
# ...
target_link_libraries(YOUR_TARGET seqan::seqan)

These are all the available headers. Some of these ones might be non-public; make sure of it by visiting the seqan homepage listed above:

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