# filelist

dirname: /usr/include/seqan3/io/sequence_file
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filenames:
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dirname: /usr/include/seqan3/contrib/stream
filetypes: fffffff
filenames:
  bgzf_istream.hpp/bgzf_ostream.hpp/bgzf_stream_util.hpp/bz2_istream.hpp/bz2_ostream.hpp/gz_istream.hpp/gz_ostream.hpp


dirname: /usr/include/seqan3/alignment/pairwise
filetypes: ffffffdfffd
filenames:
  align_pairwise.hpp/align_result_selector.hpp/alignment_algorithm.hpp/alignment_configurator.hpp/alignment_result.hpp/all.hpp/detail/edit_distance_algorithm.hpp/edit_distance_fwd.hpp/edit_distance_unbanded.hpp/policy


dirname: /usr/include/seqan3/io/alignment_file
filetypes: ffffffffffffff
filenames:
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dirname: /usr/include/seqan3/alphabet/aminoacid
filetypes: ffffffffff
filenames:
  aa10li.hpp/aa10murphy.hpp/aa20.hpp/aa27.hpp/all.hpp/aminoacid_base.hpp/concept.hpp/translation.hpp/translation_details.hpp/translation_genetic_code.hpp


dirname: /usr/include/seqan3/alignment/configuration
filetypes: fffffffffffffff
filenames:
  align_config_band.hpp/align_config_debug.hpp/align_config_edit.hpp/align_config_gap_cost_affine.hpp/align_config_method.hpp/align_config_min_score.hpp/align_config_on_result.hpp/align_config_output.hpp/align_config_parallel.hpp/align_config_result_type.hpp/align_config_score_type.hpp/align_config_scoring_scheme.hpp/align_config_vectorised.hpp/all.hpp/detail.hpp


dirname: /usr/include/seqan3/alphabet/quality
filetypes: ffffffff
filenames:
  aliases.hpp/all.hpp/concept.hpp/phred42.hpp/phred63.hpp/phred68legacy.hpp/qualified.hpp/quality_base.hpp


dirname: /usr/include/seqan3/alphabet/nucleotide
filetypes: fffffffffff
filenames:
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dirname: /usr/include/seqan3/alignment/pairwise/policy
filetypes: ffffffff
filenames:
  affine_gap_init_policy.hpp/affine_gap_policy.hpp/alignment_matrix_policy.hpp/all.hpp/find_optimum_policy.hpp/scoring_scheme_policy.hpp/simd_affine_gap_policy.hpp/simd_find_optimum_policy.hpp


dirname: /usr/include/seqan3/core
filetypes: fdffdfdfdfdfffdfdd
filenames:
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dirname: /usr/include/seqan3/alignment/scoring
filetypes: ffdffff
filenames:
  all.hpp/aminoacid_scoring_scheme.hpp/detail/gap_scheme.hpp/nucleotide_scoring_scheme.hpp/scoring_scheme_base.hpp/scoring_scheme_concept.hpp


dirname: /usr/include/seqan3/core/algorithm
filetypes: ffffffffdf
filenames:
  algorithm_result_generator_range.hpp/all.hpp/bound.hpp/concept.hpp/configuration.hpp/configuration_element_debug_mode.hpp/configuration_element_parallel_mode.hpp/configuration_utility.hpp/detail/pipeable_config_element.hpp


dirname: /usr/include/seqan3/search/configuration
filetypes: ffffffffff
filenames:
  all.hpp/default_configuration.hpp/detail.hpp/hit.hpp/max_error.hpp/max_error_common.hpp/on_result.hpp/output.hpp/parallel.hpp/result_type.hpp


dirname: /usr/include/seqan3/range/views
filetypes: ffffffffffffffffffffffffffffffffffffffff
filenames:
  all.hpp/as_const.hpp/async_input_buffer.hpp/char_to.hpp/chunk.hpp/complement.hpp/convert.hpp/deep.hpp/detail.hpp/drop.hpp/enforce_random_access.hpp/get.hpp/interleave.hpp/istreambuf.hpp/join.hpp/kmer_hash.hpp/minimiser.hpp/minimiser_hash.hpp/move.hpp/pairwise_combine.hpp/persist.hpp/rank_to.hpp/repeat.hpp/repeat_n.hpp/single_pass_input.hpp/slice.hpp/take.hpp/take_exactly.hpp/take_line.hpp/take_until.hpp/to.hpp/to_char.hpp/to_lower.hpp/to_rank.hpp/to_upper.hpp/translate.hpp/translate_join.hpp/trim_quality.hpp/type_reduce.hpp/zip.hpp


dirname: /usr/include/sdsl
filenames:
  CMakeLists.txt/bit_vector_il.hpp/bit_vectors.hpp/bits.hpp/bp_support.hpp/bp_support_algorithm.hpp/bp_support_g.hpp/bp_support_gg.hpp/bp_support_sada.hpp/cereal.hpp/coder.hpp/coder_comma.hpp/coder_elias_delta.hpp/coder_elias_gamma.hpp/coder_fibonacci.hpp/config.hpp/construct.hpp/construct_bwt.hpp/construct_config.hpp/construct_isa.hpp/construct_lcp.hpp/construct_lcp_helper.hpp/construct_sa.hpp/construct_sa_se.hpp/csa_alphabet_strategy.hpp/csa_bitcompressed.hpp/csa_sada.hpp/csa_sampling_strategy.hpp/csa_wt.hpp/cst_fully.hpp/cst_iterators.hpp/cst_sada.hpp/cst_sct3.hpp/dac_vector.hpp/divsufsort.hpp/enc_vector.hpp/fast_cache.hpp/hyb_vector.hpp/int_vector.hpp/int_vector_buffer.hpp/int_vector_io_wrappers.hpp/int_vector_mapper.hpp/inv_perm_support.hpp/io.hpp/iterators.hpp/k2_treap.hpp/k2_treap_algorithm.hpp/k2_treap_helper.hpp/k2_tree.hpp/k2_tree_helper.hpp/lcp.hpp/lcp_bitcompressed.hpp/lcp_byte.hpp/lcp_dac.hpp/lcp_support_sada.hpp/lcp_support_tree.hpp/lcp_support_tree2.hpp/lcp_vlc.hpp/lcp_wt.hpp/louds_tree.hpp/memory_management.hpp/memory_tracking.hpp/nearest_neighbour_dictionary.hpp/nn_dict_dynamic.hpp/platform.hpp/qsufsort.hpp/ram_filebuf.hpp/ram_fs.hpp/rank_support.hpp/rank_support_scan.hpp/rank_support_v.hpp/rank_support_v5.hpp/rmq_succinct_sada.hpp/rmq_succinct_sct.hpp/rmq_support.hpp/rmq_support_sparse_table.hpp/rrr_helper.hpp/rrr_vector.hpp/rrr_vector_15.hpp/sd_vector.hpp/sdsl_concepts.hpp/select_support.hpp/select_support_mcl.hpp/select_support_scan.hpp/sfstream.hpp/sorted_int_stack.hpp/sorted_multi_stack_support.hpp/sorted_stack_support.hpp/structure_tree.hpp/structure_tree.hpp.cmake/suffix_array_algorithm.hpp/suffix_array_helper.hpp/suffix_arrays.hpp/suffix_tree_algorithm.hpp/suffix_tree_helper.hpp/suffix_trees.hpp/uint128_t.hpp/uint256_t.hpp/uintx_t.hpp/util.hpp/vectors.hpp/version.hpp/vlc_vector.hpp/wavelet_trees.hpp/wm_int.hpp/wt_algorithm.hpp/wt_ap.hpp/wt_blcd.hpp/wt_gmr.hpp/wt_helper.hpp/wt_huff.hpp/wt_hutu.hpp/wt_int.hpp/wt_pc.hpp/wt_rlmn.hpp

filetypes:
[cell repeats an earlier one in this file: 115 characters]


dirname: /usr/include/seqan3/core/type_traits
filetypes: ffffffffffff
filenames:
  all.hpp/basic.hpp/concept.hpp/deferred_crtp_base.hpp/function.hpp/iterator.hpp/lazy.hpp/pack.hpp/pre.hpp/range.hpp/template_inspection.hpp/transformation_trait_or.hpp


dirname: /usr/include/seqan3/alignment/matrix
filetypes: fffffdfffff
filenames:
  alignment_coordinate.hpp/alignment_optimum.hpp/alignment_trace_algorithms.hpp/all.hpp/debug_matrix.hpp/detail/edit_distance_score_matrix_full.hpp/edit_distance_trace_matrix_full.hpp/matrix_concept.hpp/row_wise_matrix.hpp/trace_directions.hpp


dirname: /usr/include/seqan3/range/container
filetypes: ffffffff
filenames:
  aligned_allocator.hpp/all.hpp/bitcompressed_vector.hpp/concatenated_sequences.hpp/concept.hpp/dynamic_bitset.hpp/small_string.hpp/small_vector.hpp


dirname: /usr/include/seqan3/core/simd/detail
filetypes: fffffff
filenames:
  builtin_simd.hpp/builtin_simd_intrinsics.hpp/default_simd_backend.hpp/default_simd_length.hpp/simd_algorithm_avx2.hpp/simd_algorithm_avx512.hpp/simd_algorithm_sse4.hpp


dirname: /usr/include/seqan3/io/detail
filetypes: fffffffff
filenames:
  ignore_output_iterator.hpp/in_file_iterator.hpp/magic_header.hpp/misc.hpp/misc_input.hpp/misc_output.hpp/out_file_iterator.hpp/record.hpp/safe_filesystem_entry.hpp


dirname: /usr/share/doc/seqan3-doc/html/search
filenames:
  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dirname: /usr/share/doc/seqan3-doc/html
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