diff options
Diffstat (limited to 'biology/seqan/pkg-plist')
| -rw-r--r-- | biology/seqan/pkg-plist | 3524 |
1 files changed, 1657 insertions, 1867 deletions
diff --git a/biology/seqan/pkg-plist b/biology/seqan/pkg-plist index 4e5828318deb..4592c53d4e0c 100644 --- a/biology/seqan/pkg-plist +++ b/biology/seqan/pkg-plist @@ -1,169 +1,227 @@ -bin/dfi -bin/insegt -bin/mason -bin/micro_razers -bin/pair_align -bin/param_chooser -bin/rabema -bin/razers -bin/razers2 -bin/rep_sep -bin/sak -bin/seqan_tcoffee -bin/seqcons -bin/snp_store -bin/splazers -bin/stellar -bin/tree_recon -include/seqan.h include/seqan/align.h -include/seqan/align/align_algorithms.h include/seqan/align/align_base.h -include/seqan/align/align_cols_base.h -include/seqan/align/align_dynprog.h -include/seqan/align/align_generated_forwards.h -include/seqan/align/align_hirschberg.h +include/seqan/align/align_cols.h +include/seqan/align/align_config.h include/seqan/align/align_iterator_base.h -include/seqan/align/align_local_dynprog.h -include/seqan/align/align_local_dynprog_banded.h -include/seqan/align/align_myers.h -include/seqan/align/align_trace.h +include/seqan/align/align_metafunctions.h +include/seqan/align/align_traceback.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_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_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/gaps_sumlist.h -include/seqan/align/hirschberg_set.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_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/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/basic_aggregates.h -include/seqan/basic/basic_allocator_chunkpool.h -include/seqan/basic/basic_allocator_interface.h -include/seqan/basic/basic_allocator_multipool.h -include/seqan/basic/basic_allocator_simple.h -include/seqan/basic/basic_allocator_singlepool.h -include/seqan/basic/basic_allocator_to_std.h -include/seqan/basic/basic_alphabet_interface.h -include/seqan/basic/basic_alphabet_interface2.h -include/seqan/basic/basic_alphabet_simple.h -include/seqan/basic/basic_alphabet_simple_tabs.h -include/seqan/basic/basic_alphabet_trait_basic.h -include/seqan/basic/basic_compare.h -include/seqan/basic/basic_converter.h -include/seqan/basic/basic_counted_ptr.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_definition.h -include/seqan/basic/basic_forwards.h -include/seqan/basic/basic_generated_forwards.h -include/seqan/basic/basic_holder.h -include/seqan/basic/basic_holder_dynamic.h -include/seqan/basic/basic_host.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_iterator_adapt_std.h -include/seqan/basic/basic_iterator_adaptor.h -include/seqan/basic/basic_iterator_base.h -include/seqan/basic/basic_iterator_position.h -include/seqan/basic/basic_iterator_simple.h -include/seqan/basic/basic_logvalue.h +include/seqan/basic/basic_math.h include/seqan/basic/basic_metaprogramming.h -include/seqan/basic/basic_operator.h include/seqan/basic/basic_parallelism.h -include/seqan/basic/basic_pointer.h -include/seqan/basic/basic_profchar.h -include/seqan/basic/basic_profile.h include/seqan/basic/basic_proxy.h -include/seqan/basic/basic_sse2.h -include/seqan/basic/basic_tag.h -include/seqan/basic/basic_testing.h -include/seqan/basic/basic_transport.h +include/seqan/basic/basic_simd_vector.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_volatile_ptr.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_generated_forwards.h -include/seqan/blast/blast_hit.h -include/seqan/blast/blast_hit_iterator.h -include/seqan/blast/blast_hsp.h -include/seqan/blast/blast_hsp_iterator.h -include/seqan/blast/blast_iterator.h -include/seqan/blast/blast_parsing.h -include/seqan/blast/blast_report.h -include/seqan/blast/blast_run.h -include/seqan/blast/blast_stream_hit.h -include/seqan/blast/blast_stream_hit_iterator.h -include/seqan/blast/blast_stream_hsp_iterator.h -include/seqan/blast/blast_stream_report.h -include/seqan/chaining.h -include/seqan/chaining/chain_base.h -include/seqan/chaining/chain_generic.h -include/seqan/chaining/chain_meta_fragment.h -include/seqan/chaining/chain_point.h -include/seqan/chaining/chain_wrapper_point.h -include/seqan/chaining/chaining_generated_forwards.h -include/seqan/chaining/fragment.h -include/seqan/chaining/geom_distribution.h -include/seqan/chaining/range_max_tree.h -include/seqan/chaining/range_tree.h -include/seqan/chaining/rmt_base.h -include/seqan/chaining/rmt_common_algos.h -include/seqan/chaining/rmt_compl_algos.h -include/seqan/chaining/rmt_def_algos.h -include/seqan/chaining/rmt_skip_base_element.h -include/seqan/chaining/rmt_skip_element.h -include/seqan/chaining/rt_base.h -include/seqan/chaining/rt_common_algos.h -include/seqan/chaining/rt_impl.h -include/seqan/chaining/rt_skip_base_element.h -include/seqan/chaining/rt_skip_element.h -include/seqan/chaining/rt_sl_base.h -include/seqan/chaining/rt_sl_compl_algos.h -include/seqan/chaining/rt_sl_def_algos.h -include/seqan/chaining/rt_sl_impl.h -include/seqan/chaining/score_chain.h -include/seqan/chaining/score_chain_sop.h -include/seqan/chaining/score_manhattan.h -include/seqan/chaining/score_zero.h -include/seqan/chaining/skip_base_element.h -include/seqan/chaining/skip_element.h -include/seqan/chaining/skip_list.h -include/seqan/chaining/skip_list_base.h -include/seqan/chaining/skip_list_dynamic.h -include/seqan/chaining/skip_list_impl.h -include/seqan/chaining/skip_list_iterator.h -include/seqan/chaining/skip_list_type.h -include/seqan/chaining/skip_pool_alloc.h -include/seqan/chaining/tree_chain.h -include/seqan/chaining/tree_chain_sop.h -include/seqan/chaining/tree_chain_utils.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_generated_forwards.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/chunk_collector.h -include/seqan/file/cstream.h -include/seqan/file/file_array.h include/seqan/file/file_base.h include/seqan/file/file_cstyle.h -include/seqan/file/file_filereader.h -include/seqan/file/file_filereaderiterator.h -include/seqan/file/file_format.h -include/seqan/file/file_format_cgviz.h -include/seqan/file/file_format_embl.h -include/seqan/file/file_format_fasta.h -include/seqan/file/file_format_fasta_align.h -include/seqan/file/file_format_genbank.h -include/seqan/file/file_format_guess.h -include/seqan/file/file_format_mmap.h -include/seqan/file/file_format_raw.h include/seqan/file/file_forwards.h -include/seqan/file/file_generated_forwards.h +include/seqan/file/file_interface.h +include/seqan/file/file_mapping.h include/seqan/file/file_page.h -include/seqan/file/file_page_raid0.h -include/seqan/file/meta.h -include/seqan/file/stream.h -include/seqan/file/stream_algorithms.h include/seqan/file/string_external.h include/seqan/file/string_mmap.h include/seqan/find.h @@ -173,9 +231,9 @@ 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_generated_forwards.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 @@ -189,50 +247,42 @@ 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/find2.h -include/seqan/find2/find2_generated_forwards.h -include/seqan/find2/find_approx_dpsearch.h -include/seqan/find2/find_approx_find_begin.h -include/seqan/find2/find_base.h -include/seqan/find2/find_exact_shiftand.h -include/seqan/find2/find_exact_simple.h -include/seqan/find2/find_finder_default.h -include/seqan/find2/find_hamming_simple.h -include/seqan/find2/find_multiple_exact_simple.h -include/seqan/find2/find_pattern_wild_shiftand.h -include/seqan/find_motif.h -include/seqan/find_motif/em_algorithm.h -include/seqan/find_motif/find_motif_base.h -include/seqan/find_motif/find_motif_epatternbranching.h -include/seqan/find_motif/find_motif_generated_forwards.h -include/seqan/find_motif/find_motif_pms1.h -include/seqan/find_motif/find_motif_pmsp.h -include/seqan/find_motif/find_motif_projection.h -include/seqan/find_motif/frequency_distribution.h -include/seqan/find_motif/profile.h -include/seqan/find_motif/pseudocount_base.h -include/seqan/find_motif/pseudocount_mode_c.h -include/seqan/find_motif/pseudocount_mode_p.h -include/seqan/find_motif/sequence_model_types.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/graph_algorithm.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/graph_algorithms_generated_forwards.h +include/seqan/graph_algorithms/kruskal.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_align_banded_gotoh.h -include/seqan/graph_align/graph_align_banded_needleman_wunsch.h -include/seqan/graph_align/graph_align_banded_smith_waterman_clump.h -include/seqan/graph_align/graph_align_base.h -include/seqan/graph_align/graph_align_config.h -include/seqan/graph_align/graph_align_generated_forwards.h -include/seqan/graph_align/graph_align_gotoh.h -include/seqan/graph_align/graph_align_hirschberg.h -include/seqan/graph_align/graph_align_interface.h -include/seqan/graph_align/graph_align_needleman_wunsch.h -include/seqan/graph_align/graph_align_smith_waterman.h -include/seqan/graph_align/graph_align_smith_waterman_clump.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 @@ -243,7 +293,6 @@ 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_msa/graph_msa_generated_forwards.h include/seqan/graph_types.h include/seqan/graph_types/graph_base.h include/seqan/graph_types/graph_drawing.h @@ -251,7 +300,6 @@ 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_fragment.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 @@ -266,44 +314,74 @@ 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_property.h -include/seqan/graph_types/graph_types_generated_forwards.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_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_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_generated_forwards.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_device.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_manual_forwards.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 @@ -316,48 +394,99 @@ 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_generated_forwards.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/cuda.h +include/seqan/misc/dequeue.h include/seqan/misc/edit_environment.h -include/seqan/misc/misc_base.h -include/seqan/misc/misc_cmdparser.h -include/seqan/misc/misc_dequeue.h -include/seqan/misc/misc_generated_forwards.h -include/seqan/misc/misc_interval_tree.h -include/seqan/misc/misc_long_word.h -include/seqan/misc/misc_map.h -include/seqan/misc/misc_parsing.h -include/seqan/misc/misc_random.h -include/seqan/misc/misc_set.h -include/seqan/misc/misc_svg.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_generated_forwards.h include/seqan/modifier/modifier_iterator.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/parallel_algorithms.h include/seqan/parallel/parallel_atomic_misc.h include/seqan/parallel/parallel_atomic_primitives.h -include/seqan/parallel/parallel_generated_forwards.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/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 @@ -365,7 +494,6 @@ 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_generated_forwards.h include/seqan/pipe/pipe_iterator.h include/seqan/pipe/pipe_joiner.h include/seqan/pipe/pipe_namer.h @@ -378,118 +506,109 @@ include/seqan/pipe/pool_mapper.h include/seqan/pipe/pool_sorter.h include/seqan/platform.h include/seqan/platform/platform_gcc.h -include/seqan/platform/platform_generated_forwards.h -include/seqan/platform/platform_mingw.h -include/seqan/platform/platform_solaris.h +include/seqan/platform/platform_icc.h +include/seqan/platform/platform_nvcc.h include/seqan/platform/platform_windows.h include/seqan/random.h -include/seqan/random/ext_MersenneTwister.h include/seqan/random/random_base.h -include/seqan/random/random_generated_forwards.h -include/seqan/random/random_geometric.h -include/seqan/random/random_lognormal.h -include/seqan/random/random_mt19937.h -include/seqan/random/random_normal.h -include/seqan/random/random_rng_functor.h -include/seqan/random/random_shuffle.h -include/seqan/random/random_uniform.h -include/seqan/refinement.h -include/seqan/refinement/graph_algorithm_refine_align.h -include/seqan/refinement/graph_algorithm_refine_aligngraph.h -include/seqan/refinement/graph_algorithm_refine_annotation.h -include/seqan/refinement/graph_algorithm_refine_exact.h -include/seqan/refinement/graph_algorithm_refine_exact_iterative.h -include/seqan/refinement/graph_algorithm_refine_fragment.h -include/seqan/refinement/graph_algorithm_refine_inexact.h -include/seqan/refinement/graph_algorithm_refine_scoring.h -include/seqan/refinement/graph_impl_align.h -include/seqan/refinement/graph_impl_align_adapt.h -include/seqan/refinement/refinement_generated_forwards.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_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_murphy10_base.h +include/seqan/reduced_aminoacid/reduced_aminoacid_murphy10_tables.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_generated_forwards.h include/seqan/score/score_matrix.h include/seqan/score/score_matrix_data.h +include/seqan/score/score_matrix_io.h include/seqan/score/score_simple.h include/seqan/seeds.h -include/seqan/seeds/banded_align.h -include/seqan/seeds/banded_chain_align.h -include/seqan/seeds/banded_chain_align_affine.h -include/seqan/seeds/global_seed_chain.h -include/seqan/seeds/memoryManager_base.h -include/seqan/seeds/memoryManager_int.h 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+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/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_std_list.h -include/seqan/sequence/adapt_std_string.h -include/seqan/sequence/adapt_std_vector.h +include/seqan/sequence/adapt_stl_container.h +include/seqan/sequence/adapt_thrust_vector.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_generated_forwards.h include/seqan/sequence/sequence_interface.h include/seqan/sequence/sequence_lexical.h include/seqan/sequence/sequence_shortcuts.h -include/seqan/sequence/sequence_stream.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_device.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_entries_unbalanced_tree.h -include/seqan/sequence_journaled/journal_entries_unbalanced_tree_iterator.h -include/seqan/sequence_journaled/journal_entries_unbalanced_tree_node.h include/seqan/sequence_journaled/journal_entry.h include/seqan/sequence_journaled/sequence_journaled.h -include/seqan/sequence_journaled/sequence_journaled_forwards.h -include/seqan/sequence_journaled/sequence_journaled_generated_forwards.h include/seqan/sequence_journaled/sequence_journaled_iterator.h +include/seqan/sequence_journaled/sequence_journaled_iterator_fast.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_generated_forwards.h include/seqan/statistics/statistics_markov_model.h include/seqan/store.h include/seqan/store/store_align.h @@ -498,1614 +617,1285 @@ 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_generated_forwards.h include/seqan/store/store_intervaltree.h include/seqan/store/store_io.h -include/seqan/store/store_io_bam.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 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