# filelist

dirname: /usr/include/seqan2/seqan/basic
filetypes: ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/score
filetypes: ffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/journaled_string_tree
filetypes: fffffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan
filetypes: dfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfddfdfdfdffdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdfdff
filenames:
  align/align.h/align_extend/align_extend.h/align_parallel/align_parallel.h/align_profile/align_profile.h/align_split/align_split.h/alignment_free/alignment_free.h/arg_parse/arg_parse.h/bam_io/bam_io.h/basic/basic.h/bed_io/bed_io.h/blast/blast.h/consensus/consensus.h/file/file.h/find/find.h/gff_io/gff_io.h/graph_algorithms/graph_algorithms.h/graph_align/graph_align.h/graph_msa/graph_msa.h/graph_types/graph_types.h/index/index.h/journaled_set/journaled_set.h/journaled_string_tree/journaled_string_tree.h/map/map.h/math/math.h/misc/modifier/modifier.h/parallel/parallel.h/parse_lm/parse_lm.h/pipe/pipe.h/platform.h/random/random.h/realign/realign.h/reduced_aminoacid/reduced_aminoacid.h/rna_io/rna_io.h/roi_io/roi_io.h/score/score.h/seeds/seeds.h/seq_io/seq_io.h/sequence/sequence.h/sequence_journaled/sequence_journaled.h/simd/simd.h/simple_intervals_io/simple_intervals_io.h/statistics/statistics.h/store/store.h/stream/stream.h/system/system.h/tabix_io/tabix_io.h/translation/translation.h/ucsc_io/ucsc_io.h/vcf_io/vcf_io.h/version.h


dirname: /usr/include/seqan2/seqan/map
filetypes: ffffffff
filenames:
  map_adapter_stl.h/map_base.h/map_chooser.h/map_skiplist.h/map_vector.h/sumlist.h/sumlist_mini.h/sumlist_skip.h


dirname: /usr/include/seqan2/seqan/file
filetypes: ffffffff
filenames:
  file_base.h/file_cstyle.h/file_forwards.h/file_interface.h/file_mapping.h/file_page.h/string_external.h/string_mmap.h


dirname: /usr/include/seqan2/seqan/consensus
filetypes: ffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/rna_io
filetypes: ffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/align_parallel
filetypes: fffffffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/journaled_set
filetypes: ffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/find
filetypes: ffffffffffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/misc
filetypes: ffffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/arg_parse
filetypes: fffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/bam_io
filetypes: ffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/store
filetypes: ffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/system
filetypes: fffffff
filenames:
  file_async.h/file_directory.h/file_forwards.h/file_sync.h/system_base.h/system_event_win.h/system_forwards.h


dirname: /usr/include/seqan2/seqan/graph_types
filetypes: ffffffffffffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/parallel
filetypes: fffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/sequence
filetypes: fffffffffffffffffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/stream
filetypes: fffffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/graph_algorithms
filetypes: ffffffffffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/simd
filetypes: fffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/align
filetypes: ffffffffffffffffffffffffffffffffffffffffffffffffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/graph_msa
filetypes: fffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/alignment_free
filetypes: fffffff
filenames:
  af_d2.h/af_d2star.h/af_d2z.h/af_n2.h/alignment_free_base.h/alignment_free_comparison.h/kmer_functions.h


dirname: /usr/include/seqan2/seqan/sequence_journaled
filetypes: fffff
filenames:
  journal_entries_sorted_array.h/journal_entry.h/sequence_journaled.h/sequence_journaled_iterator.h/sequence_journaled_iterator_fast.h


dirname: /usr/include/seqan2/seqan/modifier
filetypes: ffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/graph_align
filetypes: ffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/pipe
filetypes: ffffffffffffffff
filenames:
  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


dirname: /usr/include/seqan2/seqan/seeds
filetypes: ffffffffffffffffffff
filenames:
  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


dirname: /usr/share/javadoc/sequence-library/de/regnis/q/sequence/core/class-use
filetypes: ffffffff
filenames:
  QSequenceAlgorithm.html/QSequenceAssert.html/QSequenceCancelledException.html/QSequenceCanceller.html/QSequenceDummyCanceller.html/QSequenceException.html/QSequenceMedia.html/QSequenceSnakeRegister.html


dirname: /usr/share/javadoc/sequence-library/de/regnis/q/sequence/line/diff
filetypes: ffffffdffff
filenames:
  QDiffGenerator.html/QDiffGeneratorFactory.html/QDiffManager.html/QDiffNormalGenerator.html/QDiffSequenceGenerator.html/QDiffUniGenerator.html/class-use/package-frame.html/package-summary.html/package-tree.html/package-use.html


dirname: /usr/share/javadoc/sequence-library/de/regnis/q/sequence/class-use
filetypes: ffffffff
filenames:
  QSequenceCommonBlockFactory.html/QSequenceCommonBlocks.html/QSequenceDifference.html/QSequenceDifferenceBlock.html/QSequenceDifferenceBlockShifter.html/QSequenceDifferenceBlockUtils.html/QSequenceSimpleLCS.html/QSequenceSimpleLCSCommand.html


dirname: /usr/share/javadoc/sequence-library/de/regnis/q/sequence/line
filetypes: fffffffffffddffffd
filenames:
  QSequenceLine.html/QSequenceLineCache.html/QSequenceLineFixedTempDirectoryFactory.html/QSequenceLineMedia.html/QSequenceLineRAByteData.html/QSequenceLineRAData.html/QSequenceLineRAFileData.html/QSequenceLineRandomAccessFileFactory.html/QSequenceLineResult.html/QSequenceLineSystemTempDirectoryFactory.html/QSequenceLineTempDirectoryFactory.html/class-use/diff/package-frame.html/package-summary.html/package-tree.html/package-use.html/simplifier


dirname: /usr/share/javadoc/sequence-library/de/regnis/q/sequence/line/diff/class-use
filetypes: ffffff
filenames:
  QDiffGenerator.html/QDiffGeneratorFactory.html/QDiffManager.html/QDiffNormalGenerator.html/QDiffSequenceGenerator.html/QDiffUniGenerator.html


dirname: /usr/share/javadoc/sequence-library/de/regnis/q/sequence/media/class-use
filetypes: ffffffffffffffff
filenames:
  QSequenceCachableMedia.html/QSequenceCachableMediaGetter.html/QSequenceCachableMediaLeftGetter.html/QSequenceCachableMediaRightGetter.html/QSequenceCachingMedia.html/QSequenceCachingMediaSymbolMap.html/QSequenceDiscardingMedia.html/QSequenceDiscardingMediaBlock.html/QSequenceDiscardingMediaConfusionDetector.html/QSequenceDiscardingMediaLeftBlock.html/QSequenceDiscardingMediaNoConfusionDectector.html/QSequenceDiscardingMediaRightBlock.html/QSequenceIntMedia.html/QSequenceMediaComparer.html/QSequenceMediaDummyIndexTransformer.html/QSequenceMediaIndexTransformer.html


dirname: /usr/share/javadoc/sequence-library/de/regnis/q/sequence/line/simplifier/class-use
filetypes: ffffff
filenames:
  QSequenceLineDummySimplifier.html/QSequenceLineEOLUnifyingSimplifier.html/QSequenceLineSimplifier.html/QSequenceLineTeeSimplifier.html/QSequenceLineWhiteSpaceReducingSimplifier.html/QSequenceLineWhiteSpaceSkippingSimplifier.html


dirname: /usr/share/javadoc/sequence-library/de/regnis/q/sequence/core
filetypes: ffffffffdffff
filenames:
  QSequenceAlgorithm.html/QSequenceAssert.html/QSequenceCancelledException.html/QSequenceCanceller.html/QSequenceDummyCanceller.html/QSequenceException.html/QSequenceMedia.html/QSequenceSnakeRegister.html/class-use/package-frame.html/package-summary.html/package-tree.html/package-use.html


dirname: /usr/share/javadoc/sequence-library/de/regnis/q/sequence/line/class-use
filetypes: fffffffffff
filenames:
  QSequenceLine.html/QSequenceLineCache.html/QSequenceLineFixedTempDirectoryFactory.html/QSequenceLineMedia.html/QSequenceLineRAByteData.html/QSequenceLineRAData.html/QSequenceLineRAFileData.html/QSequenceLineRandomAccessFileFactory.html/QSequenceLineResult.html/QSequenceLineSystemTempDirectoryFactory.html/QSequenceLineTempDirectoryFactory.html


dirname: /usr/share/javadoc/sequence-library/de/regnis/q/sequence/media
filetypes: ffffffffffffffffdffff
filenames:
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dirname: /usr/share/javadoc/sequence-library
filetypes: fffdfffffffffff
filenames:
  allclasses-frame.html/allclasses-noframe.html/constant-values.html/de/deprecated-list.html/help-doc.html/index-all.html/index.html/overview-frame.html/overview-summary.html/overview-tree.html/package-list/script.js/serialized-form.html/stylesheet.css


dirname: /usr/share/javadoc/sequence-library/de/regnis/q/sequence/line/simplifier
filetypes: ffffffdffff
filenames:
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dirname: /usr/share/javadoc/sequence-library/de/regnis/q/sequence
filetypes: ffffffffddddffff
filenames:
  QSequenceCommonBlockFactory.html/QSequenceCommonBlocks.html/QSequenceDifference.html/QSequenceDifferenceBlock.html/QSequenceDifferenceBlockShifter.html/QSequenceDifferenceBlockUtils.html/QSequenceSimpleLCS.html/QSequenceSimpleLCSCommand.html/class-use/core/line/media/package-frame.html/package-summary.html/package-tree.html/package-use.html


dirname: /usr/share/fonts/serafettin-cartoon
filetypes: gffffffff
filenames:
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dirname: /usr/include/serdisplib
filetypes: fffffff
filenames:
  serdisp.h/serdisp_colour.h/serdisp_connect.h/serdisp_control.h/serdisp_messages.h/serdisp_parport.h/serdisp_tools.h


dirname: /usr/share/javadoc/serp/serp/bytecode/class-use
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