[med-svn] [spades] 02/09: Merge tag 'upstream/3.8.0+dfsg'
Sascha Steinbiss
sascha at steinbiss.name
Mon Jun 6 22:54:15 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch master
in repository spades.
commit 78b8a93440f3512e714bf936e027c029797aa5ff
Merge: 44766e6 5dac0a3
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Tue May 31 21:50:31 2016 +0000
Merge tag 'upstream/3.8.0+dfsg'
Upstream version 3.8.0+dfsg
VERSION | 3 +-
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configs/debruijn/careful_mode.info | 37 +
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configs/debruijn/diploid_mode.info | 16 +
configs/debruijn/distance_estimation.info | 59 +-
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configs/debruijn/log.properties.template | 52 -
configs/debruijn/mda_mode.info | 120 +
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configs/debruijn/moleculo_mode.info | 127 +
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configs/debruijn/plasmid_mode.info | 12 +
configs/debruijn/rna_mode.info | 75 +
configs/debruijn/simplification.info | 374 +--
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dipspades.py | 10 +-
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ext/src/llvm/Path.cpp | 911 ++++++++
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ext/src/llvm/Unix.h | 57 +
ext/src/llvm/YAMLParser.cpp | 2445 ++++++++++++++++++++
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manual.html | 69 +-
metaspades.py | 951 ++++++++
plasmidspades.py | 951 ++++++++
spades.py | 122 +-
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src/hammer/quake_enhanced/count.cpp | 131 --
src/hammer/quake_enhanced/count/count.cpp | 226 --
.../quake_enhanced/filter_trusted_enh/main.cpp | 106 -
src/hammer/quake_enhanced/options.cpp | 206 --
.../test_correction_quality/main.cpp | 108 -
src/hammer/valid_kmer_generator.hpp | 200 --
src/include/adt/array_vector.hpp | 625 -----
src/include/adt/bag.hpp | 87 -
src/include/adt/chained_iterator.hpp | 76 -
src/include/adt/concurrent_dsu.hpp | 296 ---
src/include/adt/filter_iterator.hpp | 49 -
src/include/adt/function_traits.hpp | 70 -
src/include/adt/iterator_range.hpp | 46 -
src/include/adt/kmer_hash_vector.hpp | 370 ---
src/include/adt/kmer_map.hpp | 942 --------
src/include/adt/kmer_set.hpp | 364 ---
src/include/adt/kmer_vector.hpp | 165 --
src/include/adt/parallel_seq_vector.hpp | 110 -
src/include/adt/pointer_iterator.hpp | 172 --
src/include/adt/queue_iterator.hpp | 143 --
src/include/adt/small_pod_vector.hpp | 379 ---
src/include/config_common.hpp | 199 --
src/include/config_singl.hpp | 55 -
src/include/copy_file.hpp | 18 -
src/include/cpp_utils.hpp | 41 -
src/include/de/conj_iterator.hpp | 140 --
src/include/de/data_divider.hpp | 140 --
src/include/de/distance_estimation.hpp | 311 ---
src/include/de/extensive_distance_estimation.hpp | 211 --
src/include/de/index_point.hpp | 455 ----
src/include/de/insert_size_refiner.hpp | 166 --
src/include/de/pair_info_filters.hpp | 271 ---
src/include/de/paired_info.hpp | 863 -------
src/include/de/paired_info_helpers.hpp | 149 --
src/include/de/peak_finder.hpp | 386 ---
src/include/de/smoothing_distance_estimation.hpp | 221 --
src/include/de/weighted_distance_estimation.hpp | 115 -
src/include/file_limit.hpp | 33 -
src/include/func.hpp | 69 -
src/include/graph_print_utils.hpp | 328 ---
src/include/io/bam_parser.hpp | 67 -
src/include/io/bam_reader.hpp | 105 -
src/include/io/binary_converter.hpp | 295 ---
src/include/io/binary_streams.hpp | 357 ---
.../io/careful_filtering_reader_wrapper.hpp | 183 --
src/include/io/converting_reader_wrapper.hpp | 120 -
src/include/io/delegating_reader_wrapper.hpp | 64 -
src/include/io/easy_reader.hpp | 122 -
src/include/io/fasta_fastq_gz_parser.hpp | 165 --
src/include/io/file_reader.hpp | 129 --
src/include/io/filtering_reader_wrapper.hpp | 148 --
src/include/io/io_helper.hpp | 118 -
src/include/io/ireader.hpp | 116 -
src/include/io/ireadstream.hpp | 168 --
src/include/io/is_corrupting_wrapper.hpp | 33 -
src/include/io/kmer_iterator.hpp | 54 -
src/include/io/library.hpp | 392 ----
src/include/io/mmapped_reader.hpp | 360 ---
src/include/io/mmapped_writer.hpp | 171 --
src/include/io/modifying_reader_wrapper.hpp | 113 -
src/include/io/mpmc_bounded.hpp | 149 --
src/include/io/multifile_reader.hpp | 99 -
src/include/io/orientation.hpp | 93 -
src/include/io/osequencestream.hpp | 367 ---
src/include/io/paired_read.hpp | 186 --
src/include/io/paired_readers.hpp | 251 --
src/include/io/parser.hpp | 145 --
src/include/io/rc_reader_wrapper.hpp | 137 --
src/include/io/read.hpp | 231 --
src/include/io/read_processor.hpp | 200 --
src/include/io/read_stream_vector.hpp | 182 --
src/include/io/sam/sam_reader.hpp | 49 -
src/include/io/sequence_reader.hpp | 77 -
src/include/io/single_read.hpp | 331 ---
src/include/io/splitting_wrapper.hpp | 75 -
src/include/io/vector_reader.hpp | 60 -
src/include/io/wrapper_collection.hpp | 115 -
src/include/levenshtein.hpp | 238 --
src/include/log.hpp | 33 -
src/include/logger/log_writers.hpp | 38 -
src/include/logger/logger.hpp | 149 --
src/include/memory_limit.hpp | 91 -
src/include/mph_index/bitpair_vector.hpp | 103 -
src/include/mph_index/common.hpp | 66 -
src/include/mph_index/hypergraph_sorter_seq.hpp | 130 --
src/include/mph_index/kmer_index.hpp | 530 -----
src/include/mph_index/mphf.hpp | 136 --
src/include/omni/action_handlers.hpp | 345 ---
src/include/omni/basic_edge_conditions.hpp | 268 ---
src/include/omni/bulge_remover.hpp | 781 -------
src/include/omni/complex_bulge_remover.hpp | 1162 ----------
src/include/omni/complex_tip_clipper.hpp | 116 -
.../omni/concurrent_algo/bulge_remover_factory.hpp | 100 -
.../concurrent_algo/component_algorithm_runner.hpp | 130 --
.../concurrent_conjugate_graph_component.hpp | 121 -
.../concurrent_algo/concurrent_edge_algorithm.hpp | 193 --
.../concurrent_algo/concurrent_graph_component.hpp | 472 ----
.../conjugate_vertex_glued_graph.hpp | 124 -
.../omni/concurrent_algo/devisible_tree.hpp | 320 ---
.../sequential_algorihtm_factory.hpp | 38 -
.../omni/concurrent_algo/sequential_algorithm.hpp | 37 -
src/include/omni/coverage.hpp | 342 ---
.../omni/dijkstra_tools/dijkstra_algorithm.hpp | 288 ---
.../omni/dijkstra_tools/dijkstra_helper.hpp | 163 --
.../omni/dijkstra_tools/dijkstra_settings.hpp | 117 -
.../omni/dijkstra_tools/length_calculator.hpp | 112 -
.../omni/dijkstra_tools/neighbours_iterator.hpp | 164 --
.../omni/dijkstra_tools/vertex_process_checker.hpp | 72 -
.../omni/dijkstra_tools/vertex_put_checker.hpp | 63 -
src/include/omni/edge_labels_handler.hpp | 222 --
src/include/omni/edges_position_handler.hpp | 208 --
src/include/omni/erroneous_connection_remover.hpp | 381 ---
src/include/omni/graph_component.hpp | 198 --
src/include/omni/graph_core.hpp | 620 -----
src/include/omni/graph_iterators.hpp | 446 ----
src/include/omni/graph_processing_algorithm.hpp | 259 ---
src/include/omni/id_track_handler.hpp | 110 -
src/include/omni/loop_killer.hpp | 218 --
src/include/omni/loop_resolver.hpp | 75 -
src/include/omni/mapping_path.hpp | 227 --
src/include/omni/mf_ec_remover.hpp | 508 ----
src/include/omni/observable_graph.hpp | 497 ----
src/include/omni/omni_tools.hpp | 411 ----
src/include/omni/omni_utils.hpp | 586 -----
src/include/omni/order_and_law.hpp | 645 ------
src/include/omni/parallel_processing.hpp | 289 ---
src/include/omni/path_processor.hpp | 441 ----
src/include/omni/range.hpp | 92 -
src/include/omni/relative_coverage_remover.hpp | 674 ------
src/include/omni/splitters.hpp | 921 --------
src/include/omni/tip_clipper.hpp | 177 --
src/include/omni/visualization/graph_colorer.hpp | 340 ---
src/include/omni/visualization/graph_labeler.hpp | 304 ---
src/include/omni/visualization/graph_printer.hpp | 176 --
.../visualization/printing_parameter_storage.hpp | 81 -
src/include/omni/visualization/vertex_linker.hpp | 41 -
.../omni/visualization/visualization_utils.hpp | 210 --
src/include/omni/visualization/visualizers.hpp | 171 --
src/include/path_helper.hpp | 74 -
src/include/perfcounter.hpp | 123 -
src/include/pred.hpp | 165 --
src/include/runtime_k.hpp | 87 -
src/include/segfault_handler.hpp | 56 -
src/include/sequence/nucl.hpp | 123 -
src/include/sequence/quality.hpp | 39 -
src/include/sequence/rtseq.hpp | 724 ------
src/include/sequence/seq.hpp | 525 -----
src/include/sequence/sequence.hpp | 532 -----
src/include/sequence/sequence_tools.hpp | 159 --
src/include/sequence/simple_seq.hpp | 154 --
src/include/simple_tools.hpp | 184 --
src/include/smooth.hpp | 193 --
src/include/ssw/ssw_cpp.h | 219 --
src/include/standard_base.hpp | 142 --
src/include/verify.hpp | 34 -
src/include/xmath.h | 346 ---
src/io/CMakeLists.txt | 20 -
src/io/copy_file.cpp | 158 --
src/io/library.cpp | 179 --
src/io/logger_impl.cpp | 148 --
src/io/parser.cpp | 90 -
src/io/path_helper.cpp | 201 --
src/io/sam/read.cpp | 42 -
src/io/sam/sam_reader.cpp | 75 -
src/ionhammer/CMakeLists.txt | 33 -
src/ionhammer/HSeq.hpp | 289 ---
src/ionhammer/config_struct.cpp | 70 -
src/ionhammer/config_struct.hpp | 49 -
src/ionhammer/err_helper_table.cpp | 39 -
src/ionhammer/err_helper_table.hpp | 117 -
src/ionhammer/expander.cpp | 60 -
src/ionhammer/flow_space_read.hpp | 77 -
src/ionhammer/hamcluster.cpp | 219 --
src/ionhammer/hamcluster.hpp | 192 --
src/ionhammer/kmer_data.cpp | 245 --
src/ionhammer/kmer_data.hpp | 124 -
src/ionhammer/main.cpp | 336 ---
src/ionhammer/read_corrector.hpp | 1220 ----------
src/ionhammer/seqeval/BaseHypothesisEvaluator.cpp | 302 ---
src/ionhammer/seqeval/TreephaserLite.cpp | 593 -----
src/ionhammer/subcluster.cpp | 135 --
src/ionhammer/valid_hkmer_generator.hpp | 250 --
src/modules/CMakeLists.txt | 24 +
src/modules/algorithms/CMakeLists.txt | 11 +
.../algorithms/dijkstra/dijkstra_algorithm.hpp | 288 +++
.../algorithms/dijkstra/dijkstra_helper.hpp | 163 ++
.../algorithms/dijkstra/dijkstra_settings.hpp | 117 +
.../algorithms/dijkstra/length_calculator.hpp | 112 +
.../algorithms/dijkstra/neighbours_iterator.hpp | 164 ++
.../algorithms/dijkstra/vertex_process_checker.hpp | 72 +
.../algorithms/dijkstra/vertex_put_checker.hpp | 63 +
.../algorithms/genome_consistance_checker.cpp | 238 ++
.../algorithms/genome_consistance_checker.hpp | 77 +
src/modules/algorithms/graph_construction.hpp | 179 ++
src/modules/algorithms/graph_read_correction.hpp | 187 ++
src/modules/algorithms/mismatch_shall_not_pass.hpp | 344 +++
src/modules/algorithms/path_extend/CMakeLists.txt | 18 +
.../algorithms/path_extend/extension_chooser.hpp | 1511 ++++++++++++
.../algorithms/path_extend/ideal_pair_info.hpp | 129 ++
.../algorithms/path_extend/loop_traverser.hpp | 213 ++
.../algorithms/path_extend/next_path_searcher.hpp | 1031 +++++++++
.../algorithms/path_extend/overlap_analysis.hpp | 113 +
.../algorithms/path_extend/paired_library.hpp | 179 ++
.../algorithms/path_extend/path_extend_launch.hpp | 975 ++++++++
.../algorithms/path_extend/path_extender.hpp | 1458 ++++++++++++
src/modules/algorithms/path_extend/path_filter.hpp | 134 ++
.../algorithms/path_extend/path_visualizer.hpp | 172 ++
.../algorithms/path_extend/pe_config_struct.cpp | 172 ++
.../algorithms/path_extend/pe_config_struct.hpp | 252 ++
src/modules/algorithms/path_extend/pe_io.hpp | 263 +++
src/modules/algorithms/path_extend/pe_resolver.hpp | 520 +++++
src/modules/algorithms/path_extend/pe_utils.hpp | 462 ++++
.../scaffolder2015/connection_condition2015.cpp | 144 ++
.../scaffolder2015/connection_condition2015.hpp | 90 +
.../scaffolder2015/extension_chooser2015.cpp | 82 +
.../scaffolder2015/extension_chooser2015.hpp | 49 +
.../path_extend/scaffolder2015/scaffold_graph.cpp | 275 +++
.../path_extend/scaffolder2015/scaffold_graph.hpp | 234 ++
.../scaffolder2015/scaffold_graph_constructor.cpp | 77 +
.../scaffolder2015/scaffold_graph_constructor.hpp | 0
.../scaffolder2015/scaffold_graph_visualizer.cpp | 72 +
.../scaffolder2015/scaffold_graph_visualizer.hpp | 73 +
.../path_extend/split_graph_pair_info.hpp | 449 ++++
.../algorithms}/path_extend/utils/CMakeLists.txt | 0
.../algorithms}/path_extend/utils/find_aligns.py | 0
.../path_extend/utils/find_single_threshold.py | 0
.../path_extend/utils/paired_info_checker.cpp | 204 ++
.../path_extend/utils/run_all_parametrs.py | 0
.../algorithms/path_extend/weight_counter.hpp | 544 +++++
.../algorithms/simplification/bulge_remover.hpp | 783 +++++++
src/modules/algorithms/simplification/cleaner.hpp | 43 +
.../simplification/complex_bulge_remover.hpp | 1162 ++++++++++
.../simplification/complex_tip_clipper.hpp | 153 ++
.../algorithms/simplification/compressor.hpp | 141 ++
.../simplification/dominated_set_finder.hpp | 137 ++
.../simplification/ec_threshold_finder.hpp | 152 ++
.../erroneous_connection_remover.hpp | 567 +++++
.../algorithms/simplification/mf_ec_remover.hpp | 514 ++++
.../parallel_simplification_algorithms.hpp | 820 +++++++
.../simplification/relative_coverage_remover.hpp | 674 ++++++
.../algorithms/simplification/tip_clipper.hpp | 269 +++
src/modules/assembly_graph/CMakeLists.txt | 12 +
.../components}/component_filters.hpp | 0
.../components/connected_component.cpp | 76 +
.../components/connected_component.hpp | 26 +
.../assembly_graph/components/graph_component.hpp | 198 ++
.../assembly_graph/components/splitters.hpp | 921 ++++++++
.../assembly_graph/graph_alignment/edge_index.hpp | 112 +
.../assembly_graph/graph_alignment/kmer_map.hpp | 151 ++
.../assembly_graph/graph_alignment/kmer_mapper.hpp | 234 ++
.../graph_alignment/kmer_mapper_logger.hpp | 45 +
.../graph_alignment/long_read_mapper.hpp | 190 ++
.../graph_alignment/long_read_storage.hpp | 376 +++
.../graph_alignment/pacbio/pac_index.hpp | 834 +++++++
.../graph_alignment/pacbio/pacbio_gap_closer.hpp | 394 ++++
.../pacbio/pacbio_read_structures.hpp | 326 +++
.../graph_alignment/sequence_mapper.hpp | 408 ++++
.../graph_alignment/sequence_mapper_notifier.hpp | 175 ++
.../graph_alignment/short_read_mapper.hpp | 98 +
.../assembly_graph/graph_core/action_handlers.hpp | 347 +++
.../graph_core/basic_graph_stats.hpp | 53 +
.../graph_core}/construction_helper.hpp | 0
src/modules/assembly_graph/graph_core/coverage.hpp | 343 +++
.../assembly_graph/graph_core/debruijn_data.hpp | 170 ++
.../assembly_graph/graph_core/directions.hpp | 132 ++
src/modules/assembly_graph/graph_core/graph.hpp | 110 +
.../assembly_graph/graph_core/graph_core.hpp | 620 +++++
.../assembly_graph/graph_core/graph_iterators.hpp | 408 ++++
.../assembly_graph/graph_core/observable_graph.hpp | 499 ++++
.../assembly_graph/graph_core/order_and_law.hpp | 644 ++++++
.../graph_support/basic_edge_conditions.hpp | 272 +++
.../graph_support/basic_vertex_conditions.hpp | 52 +
.../assembly_graph/graph_support/chimera_stats.hpp | 266 +++
.../assembly_graph/graph_support/comparators.hpp | 62 +
.../assembly_graph/graph_support/contig_output.hpp | 421 ++++
.../graph_support/detail_coverage.hpp | 258 +++
.../graph_support/genomic_quality.hpp | 554 +++++
.../graph_support/graph_processing_algorithm.hpp | 262 +++
.../graph_support}/marks_and_locks.hpp | 0
.../graph_support/parallel_processing.hpp | 290 +++
.../graph_support}/scaff_supplementary.cpp | 0
.../graph_support/scaff_supplementary.hpp | 77 +
.../handlers/edge_labels_handler.hpp | 226 ++
.../handlers/edges_position_handler.hpp | 207 ++
.../assembly_graph/handlers/id_track_handler.hpp | 110 +
.../assembly_graph/paths/bidirectional_path.cpp | 21 +
.../assembly_graph/paths/bidirectional_path.hpp | 1087 +++++++++
src/modules/assembly_graph/paths/mapping_path.hpp | 227 ++
src/modules/assembly_graph/paths/path_finders.hpp | 124 +
.../assembly_graph/paths/path_processor.hpp | 441 ++++
src/modules/assembly_graph/paths/path_utils.hpp | 128 +
src/modules/assembly_graph/stats/picture_dump.hpp | 426 ++++
src/modules/assembly_graph/stats/statistics.hpp | 273 +++
.../debruijn_graph/debruijn_graph_constructor.hpp | 555 +++++
.../debruijn_graph/early_simplification.hpp | 269 +++
.../indices/edge_index_builders.hpp | 179 ++
.../data_structures/indices/edge_info_updater.hpp | 107 +
.../data_structures/indices/edge_multi_index.hpp | 161 ++
.../indices/edge_position_index.hpp | 191 ++
.../data_structures}/indices/editable_index.hpp | 0
.../data_structures}/indices/key_with_hash.hpp | 0
.../indices/kmer_extension_index.hpp | 413 ++++
.../data_structures/indices/kmer_splitters.hpp | 445 ++++
.../data_structures/indices/perfect_hash_map.hpp | 396 ++++
.../data_structures/indices/storing_traits.hpp | 61 +
.../data_structures}/indices/values.hpp | 0
.../data_structures/mph_index/CMakeLists.txt | 13 +
.../data_structures}/mph_index/base_hash.hpp | 0
.../data_structures/mph_index/bitpair_vector.cpp | 77 +
.../data_structures/mph_index/bitpair_vector.hpp | 27 +
src/modules/data_structures/mph_index/common.hpp | 66 +
.../data_structures}/mph_index/emphf_config.hpp | 0
.../data_structures}/mph_index/hypergraph.hpp | 0
.../mph_index/hypergraph_sorter_seq.hpp | 130 ++
.../data_structures/mph_index/kmer_index.hpp | 530 +++++
src/modules/data_structures/mph_index/mphf.hpp | 136 ++
.../mph_index/ranked_bitpair_vector.hpp | 0
.../data_structures/sequence/CMakeLists.txt | 10 +
.../data_structures/sequence/genome_storage.cpp | 45 +
.../data_structures/sequence/genome_storage.hpp | 33 +
src/modules/data_structures/sequence/nucl.hpp | 123 +
src/modules/data_structures/sequence/quality.hpp | 39 +
src/modules/data_structures/sequence/rtseq.hpp | 736 ++++++
src/modules/data_structures/sequence/runtime_k.hpp | 47 +
src/modules/data_structures/sequence/seq.hpp | 529 +++++
.../data_structures}/sequence/seq_common.hpp | 0
src/modules/data_structures/sequence/sequence.hpp | 542 +++++
.../data_structures/sequence/sequence_tools.hpp | 159 ++
.../data_structures/sequence/simple_seq.hpp | 154 ++
src/modules/dev_support/CMakeLists.txt | 13 +
src/modules/dev_support/autocompletion.cpp | 51 +
src/modules/dev_support/autocompletion.hpp | 16 +
src/modules/dev_support/copy_file.cpp | 158 ++
src/modules/dev_support/copy_file.hpp | 18 +
src/modules/dev_support/cpp_utils.hpp | 40 +
src/modules/dev_support/file_limit.hpp | 33 +
src/modules/dev_support/func.hpp | 69 +
src/modules/dev_support/log.hpp | 33 +
src/modules/dev_support/logger/log_writers.hpp | 43 +
src/modules/dev_support/logger/logger.hpp | 149 ++
src/modules/dev_support/logger/logger_impl.cpp | 148 ++
src/modules/dev_support/md5.h | 393 ++++
src/{include => modules/dev_support}/memory.hpp | 0
src/modules/dev_support/memory_limit.hpp | 97 +
.../dev_support}/openmp_wrapper.h | 0
.../dev_support}/parallel_wrapper.hpp | 0
src/modules/dev_support/path_helper.cpp | 249 ++
src/modules/dev_support/path_helper.hpp | 74 +
src/modules/dev_support/perfcounter.hpp | 123 +
src/modules/dev_support/range.hpp | 92 +
src/modules/dev_support/segfault_handler.hpp | 58 +
src/modules/dev_support/simple_tools.hpp | 184 ++
.../dev_support}/stacktrace.hpp | 0
src/modules/dev_support/standard_base.hpp | 140 ++
src/modules/dev_support/verify.hpp | 33 +
src/modules/empty.cpp | 0
src/modules/io/CMakeLists.txt | 16 +
src/modules/io/dataset_support/dataset_readers.hpp | 122 +
src/modules/io/dataset_support/read_converter.hpp | 360 +++
src/modules/io/graph_io/graph_print_utils.hpp | 328 +++
src/modules/io/kmers_io/kmer_iterator.hpp | 54 +
src/modules/io/kmers_io/mmapped_reader.hpp | 396 ++++
src/modules/io/kmers_io/mmapped_writer.hpp | 191 ++
src/modules/io/reads/paired_read.hpp | 186 ++
src/modules/io/reads/read.hpp | 244 ++
src/modules/io/reads/single_read.hpp | 334 +++
src/modules/io/reads_io/binary_converter.hpp | 295 +++
src/modules/io/reads_io/binary_streams.hpp | 357 +++
.../reads_io/careful_filtering_reader_wrapper.hpp | 183 ++
.../io/reads_io/converting_reader_wrapper.hpp | 121 +
.../io/reads_io}/cutting_reader_wrapper.hpp | 0
.../io/reads_io/delegating_reader_wrapper.hpp | 64 +
src/modules/io/reads_io/easy_reader.hpp | 122 +
src/modules/io/reads_io/fasta_fastq_gz_parser.hpp | 165 ++
src/modules/io/reads_io/file_reader.hpp | 129 ++
.../io/reads_io/filtering_reader_wrapper.hpp | 148 ++
src/modules/io/reads_io/io_helper.hpp | 118 +
src/modules/io/reads_io/ireader.hpp | 117 +
src/modules/io/reads_io/ireadstream.hpp | 170 ++
src/modules/io/reads_io/is_corrupting_wrapper.hpp | 33 +
.../io/reads_io/modifying_reader_wrapper.hpp | 114 +
src/modules/io/reads_io/mpmc_bounded.hpp | 153 ++
src/modules/io/reads_io/multifile_reader.hpp | 99 +
src/modules/io/reads_io/orientation.hpp | 93 +
src/modules/io/reads_io/osequencestream.hpp | 374 +++
src/modules/io/reads_io/paired_readers.hpp | 251 ++
src/modules/io/reads_io/parser.cpp | 90 +
src/modules/io/reads_io/parser.hpp | 145 ++
src/modules/io/reads_io/rc_reader_wrapper.hpp | 137 ++
src/modules/io/reads_io/read_processor.hpp | 201 ++
src/modules/io/reads_io/read_stream_vector.hpp | 183 ++
src/modules/io/reads_io/sequence_reader.hpp | 77 +
src/modules/io/reads_io/splitting_wrapper.hpp | 75 +
src/modules/io/reads_io/vector_reader.hpp | 61 +
src/modules/io/reads_io/wrapper_collection.hpp | 115 +
src/modules/io/sam_io/bam_parser.hpp | 67 +
src/modules/io/sam_io/bam_reader.hpp | 107 +
src/modules/io/sam_io/read.cpp | 42 +
src/{include/io/sam => modules/io/sam_io}/read.hpp | 0
src/modules/io/sam_io/sam_reader.cpp | 75 +
src/modules/io/sam_io/sam_reader.hpp | 49 +
src/modules/math/CMakeLists.txt | 14 +
src/modules/math/kmer_coverage_model.cpp | 394 ++++
src/modules/math/kmer_coverage_model.hpp | 50 +
src/modules/math/pred.hpp | 169 ++
src/modules/math/smooth.hpp | 195 ++
src/modules/math/xmath.h | 357 +++
src/modules/paired_info/CMakeLists.txt | 14 +
src/modules/paired_info/bwa_pair_info_filler.cpp | 408 ++++
src/modules/paired_info/bwa_pair_info_filler.hpp | 253 ++
src/modules/paired_info/data_divider.hpp | 137 ++
src/modules/paired_info/distance_estimation.hpp | 309 +++
src/modules/paired_info/histogram.hpp | 190 ++
src/modules/paired_info/index_point.hpp | 370 +++
src/modules/paired_info/insert_size_refiner.hpp | 165 ++
src/modules/paired_info/is_counter.hpp | 167 ++
src/modules/paired_info/pair_info_bounds.hpp | 30 +
src/modules/paired_info/pair_info_filler.hpp | 119 +
src/modules/paired_info/pair_info_filters.hpp | 271 +++
src/modules/paired_info/pair_info_improver.hpp | 279 +++
src/modules/paired_info/paired_info.hpp | 712 ++++++
src/modules/paired_info/paired_info_helpers.hpp | 142 ++
src/modules/paired_info/peak_finder.hpp | 385 +++
.../paired_info/smoothing_distance_estimation.hpp | 283 +++
src/modules/paired_info/split_path_constructor.hpp | 140 ++
.../paired_info/weighted_distance_estimation.hpp | 112 +
src/modules/paired_info/weights.hpp | 82 +
src/modules/pipeline/CMakeLists.txt | 14 +
src/modules/pipeline/config_common.hpp | 140 ++
src/modules/pipeline/config_singl.hpp | 57 +
src/modules/pipeline/config_struct.cpp | 786 +++++++
src/modules/pipeline/config_struct.hpp | 561 +++++
src/modules/pipeline/genomic_info.hpp | 48 +
src/modules/pipeline/genomic_info_filler.cpp | 149 ++
src/modules/pipeline/genomic_info_filler.hpp | 23 +
src/modules/pipeline/graph_pack.hpp | 163 ++
src/modules/pipeline/graphio.hpp | 1040 +++++++++
src/modules/pipeline/library.cpp | 137 ++
src/modules/pipeline/library.hpp | 365 +++
src/modules/pipeline/library.inl | 64 +
src/modules/pipeline/stage.cpp | 133 ++
src/modules/pipeline/stage.hpp | 165 ++
src/modules/stages/CMakeLists.txt | 12 +
src/modules/stages/construction.cpp | 69 +
src/modules/stages/construction.hpp | 23 +
src/modules/stages/simplification.cpp | 509 ++++
src/modules/stages/simplification.hpp | 34 +
.../graph_simplification.hpp | 978 ++++++++
.../simplification_settings.hpp | 105 +
.../single_cell_simplification.hpp | 110 +
src/modules/visualization/graph_colorer.hpp | 340 +++
src/modules/visualization/graph_labeler.hpp | 304 +++
src/modules/visualization/graph_printer.hpp | 176 ++
src/modules/visualization/position_filler.hpp | 91 +
.../visualization/printing_parameter_storage.hpp | 81 +
src/modules/visualization/vertex_linker.hpp | 41 +
.../visualization/visualization.hpp | 0
src/modules/visualization/visualization_utils.hpp | 210 ++
src/modules/visualization/visualizers.hpp | 173 ++
src/projects/CMakeLists.txt | 13 +
src/projects/cap/CMakeLists.txt | 47 +
src/projects/cap/assembly_compare.hpp | 520 +++++
src/projects/cap/assembly_problem_detection.hpp | 453 ++++
src/projects/cap/cap_commands.hpp | 731 ++++++
src/projects/cap/cap_config_struct.hpp | 40 +
src/projects/cap/cap_environment.hpp | 265 +++
src/projects/cap/cap_environment_manager.hpp | 493 ++++
src/projects/cap/cap_graph_pack.hpp | 33 +
src/projects/cap/cap_kmer_index.hpp | 535 +++++
src/projects/cap/cap_logger.hpp | 30 +
src/projects/cap/cap_online_visualizer.hpp | 41 +
src/projects/cap/colored_graph_construction.hpp | 397 ++++
src/projects/cap/coloring.hpp | 461 ++++
src/projects/cap/compare_standard.hpp | 47 +
src/projects/cap/comparison_utils.hpp | 208 ++
src/projects/cap/coordinates_handler.hpp | 1262 ++++++++++
src/projects/cap/deprecated/kmer_jumper.hpp | 73 +
src/projects/cap/deprecated/longseq_storage.hpp | 64 +
src/projects/cap/deprecated/tools_deprecated.cpp | 468 ++++
src/projects/cap/diff_masking.hpp | 335 +++
src/projects/cap/gene_analysis.hpp | 353 +++
src/projects/cap/genome_correction.hpp | 496 ++++
src/projects/cap/graph_traversal_constraints.hpp | 75 +
src/projects/cap/junk_cropping_reader.hpp | 54 +
src/projects/cap/longseq.hpp | 480 ++++
src/projects/cap/main.cpp | 73 +
src/projects/cap/mosaic.hpp | 1101 +++++++++
src/projects/cap/path_projector.hpp | 445 ++++
src/projects/cap/polynomial_hash.hpp | 404 ++++
src/projects/cap/repeat_masking.hpp | 544 +++++
src/projects/cap/serialization.hpp | 151 ++
src/projects/cap/simple_indel_finder.hpp | 382 +++
src/projects/cap/simple_inversion_finder.hpp | 433 ++++
src/projects/cap/stats.hpp | 1502 ++++++++++++
src/projects/cap/test_utils.hpp | 143 ++
src/projects/cap/tools.cpp | 183 ++
src/projects/cap/untangling.hpp | 345 +++
src/projects/cap/visualization.hpp | 171 ++
src/projects/corrector/CMakeLists.txt | 34 +
src/projects/corrector/config_struct.cpp | 78 +
src/projects/corrector/config_struct.hpp | 33 +
src/projects/corrector/contig_processor.cpp | 306 +++
src/projects/corrector/contig_processor.hpp | 65 +
src/projects/corrector/dataset_processor.cpp | 273 +++
src/projects/corrector/dataset_processor.hpp | 71 +
.../corrector/interesting_pos_processor.cpp | 127 +
.../corrector/interesting_pos_processor.hpp | 0
src/projects/corrector/main.cpp | 67 +
src/{ => projects}/corrector/positional_read.cpp | 0
src/{ => projects}/corrector/positional_read.hpp | 0
src/{ => projects}/corrector/variants_table.hpp | 0
src/projects/dipspades/CMakeLists.txt | 26 +
.../consensus_contigs_constructor.hpp | 332 +++
.../abstract_contig_corrector.hpp | 43 +
.../contig_correctors/close_gaps_corrector.hpp | 154 ++
.../equal_path_deletion_correction.hpp | 82 +
.../contig_correctors/incorrect_contig_remover.hpp | 43 +
.../iterative_redundant_contigs_remover.hpp | 94 +
.../contig_correctors/overlap_searcher.hpp | 541 +++++
.../contig_correctors/redundant_contig_remover.hpp | 891 +++++++
.../same_edge_deletion_corrector.hpp | 71 +
.../mapping_contig.hpp | 380 +++
.../mapping_contigs_storage.hpp | 114 +
.../overlap_graph.hpp | 1119 +++++++++
src/projects/dipspades/dipspades.hpp | 265 +++
src/projects/dipspades/dipspades_config.cpp | 132 ++
src/projects/dipspades/dipspades_config.hpp | 82 +
.../conservative_regions_searcher.hpp | 174 ++
.../conservative_regions_storage.hpp | 44 +
.../haplotype_assembly/contig_separation_utils.hpp | 515 +++++
.../haplotype_assembly/haplotype_assembler.hpp | 59 +
.../dipspades/kmer_gluing/equal_sequence_gluer.hpp | 146 ++
src/projects/dipspades/main.cpp | 110 +
.../bulge_correction_condition.hpp | 128 +
.../polymorphic_bulge_remover/bulge_gluer.hpp | 88 +
.../bulge_paths_searcher.hpp | 97 +
.../polymorphic_bulge_remover/bulge_splitter.hpp | 497 ++++
.../complex_bulge_remover.hpp | 145 ++
.../diploid_bulge_finder.hpp | 102 +
.../glue_direction_definer.hpp | 76 +
.../gluing_vertices_definer.hpp | 170 ++
.../iterative_tails_gluing.hpp | 132 ++
.../polymorphic_bulge_remover.hpp | 109 +
.../simple_bulge_remover.hpp | 51 +
src/projects/dipspades/utils/bulge_utils.hpp | 267 +++
src/projects/dipspades/utils/dijkstra_utils.hpp | 163 ++
src/projects/dipspades/utils/edge_gluer.hpp | 102 +
src/projects/dipspades/utils/element_printers.hpp | 108 +
src/projects/dipspades/utils/files_utils.cpp | 48 +
src/{ => projects}/dipspades/utils/files_utils.hpp | 0
src/projects/dipspades/utils/histogram.hpp | 104 +
src/projects/dipspades/utils/lcs_utils.hpp | 146 ++
src/projects/dipspades/utils/path_index.hpp | 68 +
src/projects/dipspades/utils/path_routines.hpp | 285 +++
src/projects/dipspades/utils/range_utils.hpp | 57 +
src/projects/dipspades/utils/redundancy_map.hpp | 235 ++
src/projects/dipspades/utils/sequence_utils.hpp | 36 +
src/projects/hammer/CMakeLists.txt | 36 +
src/projects/hammer/config_struct_hammer.cpp | 86 +
src/projects/hammer/config_struct_hammer.hpp | 89 +
src/projects/hammer/expander.cpp | 70 +
src/{ => projects}/hammer/expander.hpp | 0
.../hammer/gen_test_data/CMakeLists.txt | 0
src/{ => projects}/hammer/gen_test_data/main.cpp | 0
src/{ => projects}/hammer/globals.hpp | 0
src/projects/hammer/hamcluster.cpp | 288 +++
src/projects/hammer/hamcluster.hpp | 161 ++
.../hammer/hammer debug.launch.template | 0
.../hammer/hammer release.launch.template | 0
src/projects/hammer/hammer_tools.cpp | 274 +++
src/projects/hammer/hammer_tools.hpp | 57 +
src/projects/hammer/kmer_cluster.cpp | 656 ++++++
src/{ => projects}/hammer/kmer_cluster.hpp | 0
src/projects/hammer/kmer_data.cpp | 568 +++++
src/projects/hammer/kmer_data.hpp | 141 ++
src/projects/hammer/kmer_stat.hpp | 291 +++
src/projects/hammer/main.cpp | 286 +++
src/{ => projects}/hammer/misc/config.inp | 0
src/{ => projects}/hammer/misc/confignohdd.inp | 0
src/{ => projects}/hammer/misc/getresults.pl | 0
src/{ => projects}/hammer/misc/memusg | 0
src/{ => projects}/hammer/misc/pretty_latex.pl | 0
src/projects/hammer/parallel_radix_sort.hpp | 592 +++++
.../hammer/quake_correct/CMakeLists.txt | 0
src/projects/hammer/quake_correct/Read.cpp | 824 +++++++
src/{ => projects}/hammer/quake_correct/Read.h | 0
src/projects/hammer/quake_correct/bithash.cpp | 388 ++++
src/{ => projects}/hammer/quake_correct/bithash.h | 0
src/projects/hammer/quake_correct/correct.cpp | 897 +++++++
src/projects/hammer/quake_correct/edit.cpp | 665 ++++++
src/{ => projects}/hammer/quake_correct/edit.h | 0
src/{ => projects}/hammer/quake_correct/gzstream.C | 0
src/{ => projects}/hammer/quake_correct/gzstream.h | 0
.../hammer/quake_count/CMakeLists.txt | 0
.../hammer/quake_count/kmer_freq_info.hpp | 0
src/projects/hammer/quake_count/quake_count.cpp | 241 ++
src/projects/hammer/quake_count/quake_count_17.cpp | 238 ++
src/projects/hammer/quake_count/quake_count_19.cpp | 238 ++
src/projects/hammer/quake_count/quake_count_21.cpp | 238 ++
src/projects/hammer/quake_count/quake_count_25.cpp | 238 ++
src/projects/hammer/quake_count/quake_count_29.cpp | 238 ++
src/projects/hammer/quake_count/quake_count_33.cpp | 239 ++
src/projects/hammer/quake_count/quake_count_37.cpp | 238 ++
src/projects/hammer/quake_count/quake_count_45.cpp | 238 ++
src/projects/hammer/quake_count/quake_count_55.cpp | 240 ++
src/projects/hammer/quake_count/quake_count_65.cpp | 238 ++
src/projects/hammer/quake_count/quake_count_75.cpp | 238 ++
.../hammer/quake_count/valid_kmer_generator.hpp | 194 ++
.../hammer/quake_enhanced/CMakeLists.txt | 0
.../quake_enhanced/correct_hist/CMakeLists.txt | 0
.../hammer/quake_enhanced/correct_hist/main.cpp | 0
src/projects/hammer/quake_enhanced/count.cpp | 131 ++
.../hammer/quake_enhanced/count/CMakeLists.txt | 0
src/projects/hammer/quake_enhanced/count/count.cpp | 226 ++
.../hammer/quake_enhanced/filter_trusted.cpp | 0
.../quake_enhanced/filter_trusted/CMakeLists.txt | 0
.../hammer/quake_enhanced/filter_trusted/main.cpp | 0
.../filter_trusted_enh/CMakeLists.txt | 0
.../quake_enhanced/filter_trusted_enh/main.cpp | 106 +
.../quake_enhanced/generate_limits/CMakeLists.txt | 0
.../hammer/quake_enhanced/generate_limits/main.cpp | 0
src/{ => projects}/hammer/quake_enhanced/main.cpp | 0
src/projects/hammer/quake_enhanced/options.cpp | 206 ++
.../hammer/quake_enhanced/options.hpp | 0
.../quake_enhanced/prepare_graph/CMakeLists.txt | 0
.../quake_enhanced/prepare_graph/prepare_graph.cpp | 0
.../hammer/quake_enhanced/prepare_hist.cpp | 0
.../hammer/quake_enhanced/prepare_limits.cpp | 0
src/{ => projects}/hammer/quake_enhanced/quake.hpp | 0
.../test_correction_quality/CMakeLists.txt | 0
.../test_correction_quality/main.cpp | 108 +
src/{ => projects}/hammer/read_corrector.cpp | 0
src/{ => projects}/hammer/read_corrector.hpp | 0
src/projects/hammer/valid_kmer_generator.hpp | 200 ++
src/projects/ionhammer/CMakeLists.txt | 33 +
src/projects/ionhammer/HSeq.hpp | 289 +++
src/projects/ionhammer/config_struct.cpp | 84 +
src/projects/ionhammer/config_struct.hpp | 49 +
src/{ => projects}/ionhammer/consensus.hpp | 0
src/projects/ionhammer/err_helper_table.cpp | 39 +
src/projects/ionhammer/err_helper_table.hpp | 117 +
src/{ => projects}/ionhammer/err_helper_table.inc | 0
src/projects/ionhammer/expander.cpp | 60 +
src/{ => projects}/ionhammer/expander.hpp | 0
src/projects/ionhammer/flow_space_read.hpp | 77 +
src/projects/ionhammer/hamcluster.cpp | 219 ++
src/projects/ionhammer/hamcluster.hpp | 192 ++
src/{ => projects}/ionhammer/hkmer.hpp | 0
src/{ => projects}/ionhammer/hkmer_distance.hpp | 0
src/projects/ionhammer/kmer_data.cpp | 245 ++
src/projects/ionhammer/kmer_data.hpp | 124 +
src/projects/ionhammer/main.cpp | 332 +++
src/projects/ionhammer/read_corrector.hpp | 1220 ++++++++++
.../ionhammer/seqeval/BaseCallerUtils.h | 0
.../ionhammer/seqeval/BaseHypothesisEvaluator.cpp | 302 +++
.../ionhammer/seqeval/BaseHypothesisEvaluator.h | 0
src/projects/ionhammer/seqeval/TreephaserLite.cpp | 593 +++++
.../ionhammer/seqeval/TreephaserLite.h | 0
src/projects/ionhammer/subcluster.cpp | 135 ++
src/{ => projects}/ionhammer/subcluster.hpp | 0
src/projects/ionhammer/valid_hkmer_generator.hpp | 250 ++
src/projects/online_vis/CMakeLists.txt | 37 +
src/projects/online_vis/argument_list.hpp | 217 ++
src/projects/online_vis/base_commands.hpp | 503 ++++
src/projects/online_vis/command.hpp | 173 ++
src/projects/online_vis/command_mapping.hpp | 54 +
src/projects/online_vis/debruijn_commands.hpp | 14 +
src/projects/online_vis/debruijn_environment.hpp | 206 ++
.../online_vis/debruijn_online_visualizer.hpp | 53 +
src/projects/online_vis/drawing_commands.hpp | 113 +
.../drawing_commands/draw_connected_command.hpp | 62 +
.../drawing_commands/draw_contig_command.hpp | 126 +
.../drawing_commands/draw_missasemblies.hpp | 211 ++
.../draw_part_of_genome_command.hpp | 115 +
.../drawing_commands/draw_polymorphic_regions.hpp | 139 ++
.../drawing_commands/draw_poorly_assembled.hpp | 617 +++++
.../drawing_commands/draw_position_command.hpp | 80 +
.../drawing_commands/drawing_command.hpp | 100 +
.../drawing_commands/show_position_command.hpp | 80 +
src/projects/online_vis/environment.hpp | 58 +
src/projects/online_vis/errors.hpp | 122 +
src/projects/online_vis/history.hpp | 64 +
src/projects/online_vis/loaded_environments.hpp | 17 +
src/projects/online_vis/main.cpp | 71 +
src/projects/online_vis/online_visualizer.hpp | 167 ++
src/projects/online_vis/position_commands.hpp | 11 +
.../position_commands/clear_position_command.hpp | 35 +
.../position_commands/fill_position_command.hpp | 65 +
src/projects/online_vis/processing_commands.hpp | 66 +
src/projects/online_vis/setting_commands.hpp | 161 ++
src/projects/online_vis/standard_vis.hpp | 23 +
src/projects/online_vis/statistics_commands.hpp | 13 +
.../junction_sequence_command.hpp | 97 +
.../statistics_commands/print_contigs_stats.hpp | 220 ++
.../statistics_commands/print_edge_command.hpp | 60 +
.../statistics_commands/print_paths_command.hpp | 103 +
src/projects/online_vis/vis_logger.hpp | 28 +
src/projects/online_vis/vis_utils.hpp | 40 +
src/projects/scaffold_correction/CMakeLists.txt | 23 +
src/projects/scaffold_correction/main.cpp | 112 +
.../scaffold_correction/scaffold_correction.hpp | 333 +++
src/projects/spades/CMakeLists.txt | 32 +
src/projects/spades/chromosome_removal.cpp | 244 ++
src/projects/spades/chromosome_removal.hpp | 35 +
src/projects/spades/distance_estimation.cpp | 231 ++
src/projects/spades/distance_estimation.hpp | 24 +
src/projects/spades/gap_closer.cpp | 502 ++++
src/projects/spades/gap_closer.hpp | 33 +
src/projects/spades/launch.hpp | 120 +
src/projects/spades/main.cpp | 110 +
src/projects/spades/mismatch_correction.cpp | 27 +
src/projects/spades/mismatch_correction.hpp | 23 +
src/projects/spades/pacbio_aligning.cpp | 185 ++
src/projects/spades/pacbio_aligning.hpp | 23 +
src/projects/spades/pair_info_count.cpp | 259 +++
src/projects/spades/pair_info_count.hpp | 24 +
src/projects/spades/repeat_resolving.cpp | 96 +
src/projects/spades/repeat_resolving.hpp | 42 +
src/projects/spades/second_phase_setup.cpp | 42 +
src/projects/spades/second_phase_setup.hpp | 22 +
.../truseq_analysis/AlignmentAnalyserNew.cpp | 102 +
.../truseq_analysis/AlignmentAnalyserNew.hpp | 34 +
src/projects/truseq_analysis/CMakeLists.txt | 15 +
.../truseq_analysis/alignment_analyser.cpp | 116 +
.../truseq_analysis/alignment_analyser.hpp | 41 +
src/projects/truseq_analysis/analysis_pipeline.cpp | 140 ++
src/projects/truseq_analysis/analysis_pipeline.hpp | 39 +
.../truseq_analysis/consistent_mapping.cpp | 245 ++
src/projects/truseq_analysis/consistent_mapping.h | 90 +
src/projects/truseq_analysis/main.cpp | 95 +
src/scaffold_correction/CMakeLists.txt | 24 -
src/scaffold_correction/main.cpp | 171 --
src/scaffold_correction/scaffold_correction.hpp | 332 ---
src/spades_pipeline/corrector_logic.py | 11 +-
src/spades_pipeline/dipspades_logic.py | 3 -
src/spades_pipeline/hammer_logic.py | 85 +-
src/spades_pipeline/options_storage.py | 52 +-
src/spades_pipeline/spades_logic.py | 104 +-
src/spades_pipeline/support.py | 83 +-
src/spades_pipeline/truspades/launch_options.py | 10 +-
src/utils/adt/array_vector.hpp | 677 ++++++
src/utils/adt/bag.hpp | 87 +
src/utils/adt/chained_iterator.hpp | 76 +
src/utils/adt/concurrent_dsu.hpp | 297 +++
src/utils/adt/filter_iterator.hpp | 49 +
src/{include => utils}/adt/flat_map.hpp | 0
src/{include => utils}/adt/flat_set.hpp | 0
src/utils/adt/function_traits.hpp | 76 +
src/utils/adt/iterator_range.hpp | 50 +
src/utils/adt/kmer_hash_vector.hpp | 370 +++
src/utils/adt/kmer_vector.hpp | 179 ++
src/utils/adt/parallel_seq_vector.hpp | 110 +
.../adt/parallel_unordered_map.hpp | 0
src/utils/adt/pointer_iterator.hpp | 174 ++
src/utils/adt/queue_iterator.hpp | 143 ++
src/utils/adt/small_pod_vector.hpp | 399 ++++
src/utils/levenshtein.hpp | 241 ++
truspades.py | 21 +-
1199 files changed, 143574 insertions(+), 104584 deletions(-)
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