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Summary of changes:
LICENSE | 7 +-
README | 9 +-
VERSION | 2 +-
changelog.html | 33 +-
configs/corrector/corrector.info | 3 +-
configs/corrector/log.properties | 2 +
.../{careful_mode.info => careful_mda_mode.info} | 14 +-
configs/debruijn/careful_mode.info | 12 +-
configs/debruijn/config.info | 25 +-
configs/debruijn/log.properties | 2 +
configs/debruijn/mda_mode.info | 2 +-
configs/debruijn/meta_mode.info | 31 +-
configs/debruijn/moleculo_mode.info | 6 +-
configs/debruijn/pe_params.info | 35 +-
configs/debruijn/rna_fast_mode.info | 12 +
configs/debruijn/rna_mode.info | 80 +-
configs/debruijn/simplification.info | 36 +-
configs/debruijn/toy.info | 4 +
configs/debruijn/toy.yaml | 4 +
ext/include/ConsensusCore/Feature.hpp | 166 --
ext/include/ConsensusCore/Features.hpp | 68 -
.../ConsensusCore/Matrix/SparseMatrix-inl.hpp | 1 -
ext/include/ConsensusCore/Poa/PoaGraph.hpp | 4 +-
ext/include/ConsensusCore/Version.hpp | 1 -
ext/include/boomphf/BooPHF.h | 1422 +++++++++++++
ext/include/llvm/ADT/IntrusiveRefCntPtr.h | 2 +-
ext/include/llvm/Support/MathExtras.h | 46 +
ext/include/llvm/Support/TrailingObjects.h | 401 ++++
ext/src/ConsensusCore/CMakeLists.txt | 2 -
ext/src/ConsensusCore/Feature.cpp | 64 -
ext/src/ConsensusCore/Features.cpp | 51 -
ext/src/ConsensusCore/Matrix/DenseMatrix.cpp | 6 +-
ext/src/ConsensusCore/Matrix/SparseMatrix.cpp | 4 +-
ext/src/ConsensusCore/Poa/PoaConsensus.cpp | 7 +-
ext/src/ConsensusCore/Poa/PoaGraph.cpp | 33 +-
ext/src/ConsensusCore/Version.cpp | 2 -
manual.html | 88 +-
metaspades.py | 81 +-
plasmidspades.py | 81 +-
rnaspades.py | 81 +-
rnaspades_manual.html | 48 +-
spades.py | 81 +-
src/CMakeLists.txt | 5 +
src/cmake/options.cmake | 9 +
src/cmake/pack.cmake | 4 +-
src/common/CMakeLists.txt | 7 +-
src/common/adt/array_vector.hpp | 327 +--
src/common/adt/bag.hpp | 16 +-
src/common/adt/bf.hpp | 285 +--
src/common/adt/chained_iterator.hpp | 4 +-
src/common/adt/concurrent_dsu.hpp | 15 +-
src/common/adt/filter_iterator.hpp | 32 +-
src/common/adt/flat_map.hpp | 59 +-
src/common/adt/flat_set.hpp | 40 +-
src/common/adt/hll.hpp | 31 +-
src/common/adt/iterator_range.hpp | 11 +-
src/common/adt/kmer_hash_vector.hpp | 370 ----
src/common/adt/kmer_vector.hpp | 22 +-
src/common/adt/loser_tree.hpp | 29 +-
src/common/adt/parallel_seq_vector.hpp | 110 -
src/common/adt/parallel_unordered_map.hpp | 137 --
src/common/adt/pointer_iterator.hpp | 4 +
src/common/adt/queue_iterator.hpp | 22 +-
src/common/adt/small_pod_vector.hpp | 6 +-
.../components/connected_component.cpp | 4 +-
.../components/connected_component.hpp | 2 +-
src/common/assembly_graph/components/splitters.hpp | 33 +-
.../construction}/debruijn_graph_constructor.hpp | 367 ++--
.../construction}/early_simplification.hpp | 8 +-
src/common/assembly_graph/core/graph_core.hpp | 30 +-
src/common/assembly_graph/core/graph_iterators.hpp | 13 +-
src/common/assembly_graph/core/order_and_law.hpp | 2 +-
.../assembly_graph/dijkstra/dijkstra_algorithm.hpp | 8 +-
.../assembly_graph/graph_support/contig_output.hpp | 584 +----
.../graph_support/coverage_filling.hpp | 4 +-
.../graph_support/detail_coverage.hpp | 5 +-
.../graph_support/genomic_quality.hpp | 20 +-
.../graph_support/parallel_processing.hpp | 76 +-
.../graph_support/scaff_supplementary.cpp | 46 +-
.../graph_support/scaff_supplementary.hpp | 110 +-
.../handlers/edge_labels_handler.hpp | 2 +-
.../handlers/edges_position_handler.hpp | 30 +-
.../assembly_graph/handlers/id_track_handler.hpp | 31 +-
.../index}/edge_index_builders.hpp | 84 +-
.../index}/edge_info_updater.hpp | 4 +-
.../index}/edge_multi_index.hpp | 8 +-
.../index}/edge_position_index.hpp | 22 +-
.../assembly_graph/paths/bidirectional_path.hpp | 766 ++-----
.../paths/bidirectional_path_container.hpp | 210 ++
.../bidirectional_path_output.cpp | 71 +-
.../bidirectional_path_output.hpp | 274 ++-
.../paths/bidirectional_path_io/io_support.cpp | 100 +-
.../paths/bidirectional_path_io/io_support.hpp | 81 +-
src/common/assembly_graph/paths/mapping_path.hpp | 227 +-
src/common/assembly_graph/paths/path_processor.hpp | 17 +-
src/common/assembly_graph/stats/picture_dump.hpp | 47 +-
src/common/assembly_graph/stats/statistics.hpp | 7 +-
src/common/io/dataset_support/dataset_readers.hpp | 2 +-
src/common/io/dataset_support/read_converter.hpp | 4 +-
src/common/io/kmers/kmer_iterator.hpp | 2 +-
src/common/io/kmers/mmapped_reader.hpp | 9 +-
src/common/io/kmers/mmapped_writer.hpp | 14 +-
src/common/io/reads/binary_converter.hpp | 2 +-
src/common/io/reads/binary_streams.hpp | 4 +-
src/common/io/reads/fasta_fastq_gz_parser.hpp | 5 +
src/common/io/reads/file_reader.hpp | 4 +-
src/common/io/reads/ireadstream.hpp | 4 +
src/common/io/reads/osequencestream.hpp | 318 +--
src/common/io/reads/paired_read.hpp | 5 -
src/common/io/reads/read.hpp | 2 +-
src/common/io/reads/read_processor.hpp | 2 +-
src/common/io/reads/sequence_reader.hpp | 2 +-
src/common/io/reads/single_read.hpp | 22 +-
src/common/io/reads/wrapper_collection.hpp | 2 +-
src/common/{utils => math}/log.hpp | 0
src/common/modules/alignment/bwa_index.cpp | 10 +-
src/common/modules/alignment/edge_index.hpp | 8 +-
.../modules/alignment/edge_index_refiller.cpp | 4 +-
src/common/modules/alignment/kmer_mapper.hpp | 4 +-
.../modules/alignment/kmer_mapper_logger.hpp | 2 +-
src/common/modules/alignment/pacbio/pac_index.hpp | 281 ++-
.../alignment/pacbio/pacbio_read_structures.hpp | 60 +-
src/common/modules/alignment/rna/ss_coverage.hpp | 61 +
.../modules/alignment/rna/ss_coverage_filler.hpp | 62 +
src/common/modules/alignment/sequence_mapper.hpp | 5 +-
.../modules/alignment/sequence_mapper_notifier.hpp | 17 +-
src/common/modules/alignment/short_read_mapper.hpp | 2 +-
.../coverage_model/CMakeLists.txt | 0
.../coverage_model/kmer_coverage_model.cpp | 2 -
.../coverage_model/kmer_coverage_model.hpp | 2 -
src/common/modules/genome_consistance_checker.cpp | 610 ++++--
src/common/modules/genome_consistance_checker.hpp | 221 +-
src/common/modules/graph_construction.hpp | 36 +-
src/common/modules/graph_read_correction.hpp | 4 +-
.../modules/path_extend/extension_chooser.hpp | 269 ++-
src/common/modules/path_extend/loop_traverser.hpp | 127 +-
.../modules/path_extend/overlap_analysis.hpp | 4 +-
src/common/modules/path_extend/path_extender.hpp | 1457 ++++++-------
src/common/modules/path_extend/path_filter.hpp | 163 +-
src/common/modules/path_extend/path_visualizer.hpp | 4 +-
.../modules/path_extend/pe_config_struct.cpp | 66 +-
.../modules/path_extend/pe_config_struct.hpp | 29 +-
src/common/modules/path_extend/pe_resolver.hpp | 700 ++----
src/common/modules/path_extend/pe_utils.hpp | 156 +-
.../path_extend/pipeline/extenders_logic.cpp | 137 +-
.../path_extend/pipeline/extenders_logic.hpp | 40 +-
.../path_extend/pipeline/launch_support.cpp | 11 +-
.../path_extend/pipeline/launch_support.hpp | 18 +-
.../modules/path_extend/pipeline/launcher.cpp | 288 ++-
.../modules/path_extend/pipeline/launcher.hpp | 40 +-
.../scaffolder2015/connection_condition2015.cpp | 4 +-
.../scaffolder2015/connection_condition2015.hpp | 2 +-
.../scaffolder2015/extension_chooser2015.hpp | 2 +-
.../path_extend/scaffolder2015/path_polisher.cpp | 371 ++--
.../path_extend/scaffolder2015/path_polisher.hpp | 120 +-
.../path_extend/scaffolder2015/scaffold_graph.hpp | 2 +-
.../scaffolder2015/scaffold_graph_visualizer.cpp | 12 +-
src/common/modules/path_extend/weight_counter.hpp | 83 +-
.../modules/simplification/bulge_remover.hpp | 190 +-
src/common/modules/simplification/cleaner.hpp | 6 +
.../simplification/complex_bulge_remover.hpp | 46 +-
.../modules/simplification/complex_tip_clipper.hpp | 2 +-
src/common/modules/simplification/compressor.hpp | 2 +-
.../simplification/dominated_set_finder.hpp | 10 +-
.../modules/simplification/ec_threshold_finder.hpp | 8 +-
.../erroneous_connection_remover.hpp | 14 +-
.../parallel_simplification_algorithms.hpp | 86 +-
.../simplification/relative_coverage_remover.hpp | 14 +-
src/common/modules/simplification/tip_clipper.hpp | 14 +-
.../coverage_model => paired_info}/CMakeLists.txt | 9 +-
src/common/paired_info/distance_estimation.cpp | 176 ++
src/common/paired_info/distance_estimation.hpp | 227 +-
src/common/paired_info/histogram.hpp | 4 +-
src/common/paired_info/paired_info.hpp | 2 +-
.../paired_info/smoothing_distance_estimation.cpp | 185 ++
.../paired_info/smoothing_distance_estimation.hpp | 198 +-
src/common/paired_info/split_path_constructor.hpp | 2 +-
.../paired_info/weighted_distance_estimation.cpp | 63 +
.../paired_info/weighted_distance_estimation.hpp | 69 +-
src/common/paired_info/weights.hpp | 3 +-
src/common/pipeline/config_common.hpp | 8 +-
src/common/pipeline/config_struct.cpp | 58 +-
src/common/pipeline/config_struct.hpp | 31 +-
src/common/pipeline/genomic_info_filler.cpp | 10 +-
src/common/pipeline/graph_pack.hpp | 17 +-
src/common/pipeline/graphio.hpp | 29 +-
src/common/pipeline/library.cpp | 2 +-
src/common/pipeline/library.hpp | 10 +-
src/common/pipeline/library.inl | 2 +-
src/common/pipeline/stage.cpp | 4 +-
src/common/sequence/genome_storage.hpp | 67 +-
src/common/{utils => sequence}/levenshtein.hpp | 8 +-
src/common/{utils => sequence}/range.hpp | 7 +-
src/common/sequence/rtseq.hpp | 17 +-
src/common/sequence/seq.hpp | 10 +-
src/common/sequence/sequence.hpp | 121 +-
src/common/sequence/sequence_tools.hpp | 4 +-
src/common/sequence/simple_seq.hpp | 2 +-
src/common/stages/construction.cpp | 2 +-
src/common/stages/simplification.cpp | 47 +-
.../graph_simplification.hpp | 49 +-
.../simplification_pipeline/rna_simplification.hpp | 9 +-
src/common/utils/CMakeLists.txt | 4 +-
src/common/utils/autocompletion.cpp | 2 +-
src/common/utils/autocompletion.hpp | 2 +-
src/common/utils/cpp_utils.hpp | 5 +
.../kmer_extension_index.hpp | 53 +-
.../kmer_extension_index_builder.hpp | 9 +-
src/common/utils/{ => filesystem}/copy_file.cpp | 25 +-
src/common/utils/{ => filesystem}/copy_file.hpp | 10 +-
src/common/utils/{ => filesystem}/file_limit.hpp | 4 +
src/common/utils/{ => filesystem}/path_helper.cpp | 11 +-
src/common/utils/{ => filesystem}/path_helper.hpp | 22 +-
src/common/utils/indices/editable_index.hpp | 270 ---
src/common/utils/indices/kmer_splitters.hpp | 317 ---
.../common/utils/kmer_mph/1.cpp | 0
.../utils/{mph_index => kmer_mph}/CMakeLists.txt | 2 +-
.../utils/{mph_index => kmer_mph}/kmer_index.hpp | 33 +-
.../{mph_index => kmer_mph}/kmer_index_builder.hpp | 216 +-
.../{mph_index => kmer_mph}/kmer_index_traits.hpp | 28 +-
src/common/utils/kmer_mph/kmer_splitters.hpp | 394 ++++
src/common/utils/logger/log_writers.hpp | 44 +-
src/common/utils/logger/logger.hpp | 9 +-
src/common/utils/logger/logger_impl.cpp | 19 +-
src/common/utils/md5.h | 4 +
src/common/utils/mph_index/base_hash.hpp | 293 ---
src/common/utils/mph_index/bitpair_vector.cpp | 77 -
src/common/utils/mph_index/bitpair_vector.hpp | 27 -
src/common/utils/mph_index/common.hpp | 66 -
src/common/utils/mph_index/emphf_config.hpp | 6 -
src/common/utils/mph_index/hypergraph.hpp | 137 --
.../utils/mph_index/hypergraph_sorter_seq.hpp | 130 --
src/common/utils/mph_index/mphf.hpp | 136 --
.../utils/mph_index/ranked_bitpair_vector.hpp | 91 -
src/common/utils/{ => parallel}/openmp_wrapper.h | 0
.../utils/{ => parallel}/parallel_wrapper.hpp | 0
src/common/utils/{ => perf}/memory.hpp | 11 +-
src/common/utils/{ => perf}/memory_limit.hpp | 7 +-
src/common/utils/{ => perf}/perfcounter.hpp | 70 +-
.../utils/{indices => ph_map}/key_with_hash.hpp | 2 +-
.../utils/{indices => ph_map}/perfect_hash_map.hpp | 12 +-
.../perfect_hash_map_builder.hpp | 15 +-
.../utils/{indices => ph_map}/storing_traits.hpp | 23 +-
src/common/utils/{indices => ph_map}/values.hpp | 2 +-
src/common/utils/segfault_handler.hpp | 5 +
src/common/utils/simple_tools.hpp | 189 --
src/common/utils/stacktrace.hpp | 11 +-
src/common/utils/standard_base.hpp | 10 +-
src/common/utils/stl_utils.hpp | 141 ++
src/common/utils/verify.hpp | 7 +-
src/common/visualization/graph_labeler.hpp | 12 +-
src/common/visualization/graph_print_utils.hpp | 8 +-
src/common/visualization/position_filler.hpp | 50 +-
src/common/visualization/visualization_utils.hpp | 10 +-
src/projects/cap/assembly_compare.hpp | 2 +-
src/projects/cap/assembly_problem_detection.hpp | 6 +-
src/projects/cap/cap_commands.hpp | 8 +-
src/projects/cap/cap_environment_manager.hpp | 2 +-
src/projects/cap/cap_kmer_index.hpp | 4 +-
src/projects/cap/compare_standard.hpp | 4 +-
src/projects/cap/comparison_utils.hpp | 8 +-
src/projects/cap/deprecated/tools_deprecated.cpp | 2 +-
src/projects/cap/diff_masking.hpp | 2 +-
src/projects/cap/gene_analysis.hpp | 14 +-
src/projects/cap/genome_correction.hpp | 8 +-
src/projects/cap/longseq.hpp | 4 +-
src/projects/cap/main.cpp | 4 +-
src/projects/cap/mosaic.hpp | 8 +-
src/projects/cap/repeat_masking.hpp | 8 +-
src/projects/cap/simple_inversion_finder.hpp | 4 +-
src/projects/cap/stats.hpp | 24 +-
src/projects/cclean/CMakeLists.txt | 30 -
src/projects/cclean/adapter_index.cpp | 50 -
src/projects/cclean/adapter_index.hpp | 61 -
src/projects/cclean/additional.cpp | 69 -
src/projects/cclean/brute_force_clean.cpp | 97 -
src/projects/cclean/brute_force_clean.hpp | 72 -
src/projects/cclean/comparator.hpp | 18 -
src/projects/cclean/config_struct_cclean.cpp | 44 -
src/projects/cclean/config_struct_cclean.hpp | 42 -
src/projects/cclean/job_wrappers.cpp | 97 -
src/projects/cclean/job_wrappers.hpp | 73 -
src/projects/cclean/main.cpp | 86 -
src/projects/cclean/output.cpp | 82 -
src/projects/cclean/output.hpp | 49 -
src/projects/cclean/running_modes.cpp | 268 ---
src/projects/cclean/running_modes.hpp | 93 -
src/projects/cclean/utils.cpp | 136 --
src/projects/cclean/utils.hpp | 58 -
src/projects/cclean/valid_kmer_generator.hpp | 198 --
src/projects/corrector/config_struct.cpp | 3 +-
src/projects/corrector/config_struct.hpp | 1 +
src/projects/corrector/contig_processor.cpp | 32 +-
src/projects/corrector/contig_processor.hpp | 8 +-
src/projects/corrector/dataset_processor.cpp | 34 +-
src/projects/corrector/dataset_processor.hpp | 9 +-
.../corrector/interesting_pos_processor.hpp | 5 +
src/projects/corrector/main.cpp | 25 +-
src/projects/corrector/positional_read.hpp | 7 +-
.../consensus_contigs_constructor.hpp | 10 +-
.../contig_correctors/close_gaps_corrector.hpp | 16 +-
.../equal_path_deletion_correction.hpp | 2 +-
.../contig_correctors/incorrect_contig_remover.hpp | 2 +-
.../iterative_redundant_contigs_remover.hpp | 16 +-
.../contig_correctors/overlap_searcher.hpp | 10 +-
.../contig_correctors/redundant_contig_remover.hpp | 4 +-
.../overlap_graph.hpp | 6 +-
src/projects/dipspades/dipspades.hpp | 20 +-
src/projects/dipspades/dipspades_config.cpp | 4 +-
.../conservative_regions_searcher.hpp | 4 +-
.../haplotype_assembly/haplotype_assembler.hpp | 2 +-
src/projects/dipspades/main.cpp | 22 +-
.../polymorphic_bulge_remover.hpp | 8 +-
src/projects/dipspades/utils/bulge_utils.hpp | 2 +-
src/projects/hammer/config_struct_hammer.cpp | 2 +-
src/projects/hammer/hamcluster.cpp | 14 +-
src/projects/hammer/hamcluster.hpp | 6 +-
src/projects/hammer/hammer_tools.cpp | 2 +-
src/projects/hammer/kmer_cluster.cpp | 20 +-
src/projects/hammer/kmer_data.cpp | 28 +-
src/projects/hammer/kmer_data.hpp | 13 +-
src/projects/hammer/main.cpp | 10 +-
src/projects/hammer/parallel_radix_sort.hpp | 2 +-
src/projects/ionhammer/CMakeLists.txt | 22 +-
src/projects/ionhammer/HSeq.hpp | 230 +-
src/projects/ionhammer/comparator.py | 215 ++
src/projects/ionhammer/config_struct.cpp | 134 +-
src/projects/ionhammer/config_struct.hpp | 37 +-
src/projects/ionhammer/consensus.hpp | 12 +-
src/projects/ionhammer/err_helper_table.cpp | 18 +-
src/projects/ionhammer/err_helper_table.hpp | 50 +-
src/projects/ionhammer/expander.cpp | 60 -
src/projects/ionhammer/expander.hpp | 31 -
src/projects/ionhammer/flow_space_read.hpp | 33 +-
src/projects/ionhammer/gamma_poisson_model.cpp | 16 +
src/projects/ionhammer/gamma_poisson_model.hpp | 869 ++++++++
src/projects/ionhammer/hamcluster.cpp | 219 --
src/projects/ionhammer/hamcluster.hpp | 191 --
src/projects/ionhammer/hamcluster_1.cpp | 5 +
src/projects/ionhammer/hamcluster_1.h | 81 +
src/projects/ionhammer/hkmer.hpp | 34 +-
src/projects/ionhammer/hkmer_distance.hpp | 217 +-
src/projects/ionhammer/io_read_corrector.hpp | 230 ++
src/projects/ionhammer/kmer_data.cpp | 119 +-
src/projects/ionhammer/kmer_data.hpp | 77 +-
src/projects/ionhammer/kmer_evaluator.cpp | 53 +
src/projects/ionhammer/kmer_helpers.cpp | 5 +
src/projects/ionhammer/kmer_helpers.h | 69 +
src/projects/ionhammer/main.cpp | 497 +++--
src/projects/ionhammer/normal_quality_model.cpp | 14 +
src/projects/ionhammer/normal_quality_model.hpp | 490 +++++
src/projects/ionhammer/penalty_estimator.hpp | 326 +++
src/projects/ionhammer/quality_metrics.cpp | 5 +
src/projects/ionhammer/quality_metrics.h | 189 ++
.../ionhammer/quality_thresholds_estimator.cpp | 5 +
.../ionhammer/quality_thresholds_estimator.h | 101 +
src/projects/ionhammer/read_corrector.hpp | 563 +++--
src/projects/ionhammer/read_corrector_new.hpp | 252 +++
.../ionhammer/read_corrector_structs_new.h | 740 +++++++
src/projects/ionhammer/reference.cpp | 1 +
src/projects/ionhammer/reference.h | 59 +
src/projects/ionhammer/subcluster.cpp | 283 ++-
src/projects/ionhammer/subcluster.hpp | 100 +-
src/projects/ionhammer/thread_utils.h | 57 +
src/projects/ionhammer/valid_hkmer_generator.hpp | 130 +-
src/projects/mph_test/main.cpp | 29 +-
src/projects/mts/CMakeLists.txt | 3 +-
src/projects/mts/Common.snake | 98 +-
src/projects/mts/README | 15 +-
src/projects/mts/Reassembly.snake | 74 +
src/projects/mts/Snakefile | 413 ++--
src/projects/mts/Stats.snake | 395 ++--
src/projects/mts/annotation.hpp | 30 +-
src/projects/mts/config.yaml | 34 +-
src/projects/mts/contig_abundance.cpp | 80 +-
src/projects/mts/contig_abundance.hpp | 43 +-
src/projects/mts/contig_abundance_counter.cpp | 61 +-
.../quake_correct => mts/gzstream}/gzstream.C | 6 +-
.../quake_correct => mts/gzstream}/gzstream.h | 7 -
src/projects/mts/kmer_multiplicity_counter.cpp | 14 +-
src/projects/mts/logger.hpp | 2 +-
src/projects/mts/mts.py | 71 +-
src/projects/mts/multirun.py | 84 +
src/projects/mts/prop_binning.cpp | 84 +-
src/projects/mts/propagate.cpp | 120 +-
src/projects/mts/propagate.hpp | 10 +-
src/projects/mts/read_binning.cpp | 74 +-
src/projects/mts/read_binning.hpp | 31 +-
src/projects/mts/scripts/Dataset_analysis.ipynb | 2246 ++++++++++++++++++++
src/projects/mts/scripts/bhtsne.py | 242 +++
src/projects/mts/scripts/bin_profiles.py | 12 +
src/projects/mts/scripts/calc_kmers_mpl.py | 38 -
src/projects/mts/scripts/canopy_launch.sh | 17 -
src/projects/mts/scripts/choose_bins.py | 20 +
src/projects/mts/scripts/choose_samples.py | 115 +-
src/projects/mts/scripts/clusters2csv.py | 22 +
src/projects/mts/scripts/combine_contigs.py | 8 +-
src/projects/mts/scripts/common.py | 63 +-
src/projects/mts/scripts/contig_name_filter.py | 30 +
src/projects/mts/scripts/convert_output.py | 53 +
src/projects/mts/scripts/cut_fasta.py | 45 +
src/projects/mts/scripts/filter_bin.py | 17 +
src/projects/mts/scripts/filter_nucmer.py | 62 +-
src/projects/mts/scripts/gather_stats.py | 84 +-
src/projects/mts/scripts/gen_samples.py | 77 +-
src/projects/mts/scripts/make_input.py | 53 +-
src/projects/mts/scripts/make_points_matrix.py | 35 -
src/projects/mts/scripts/parse_output.py | 58 -
src/projects/mts/scripts/pca.R | 47 +-
src/projects/mts/scripts/ref_stats.sh | 63 -
src/projects/mts/scripts/run_tsne.py | 239 +++
src/projects/mts/scripts/split_bins.py | 18 +-
src/projects/mts/scripts/validate.pl | 404 ++++
src/projects/mts/stats.cpp | 8 +-
src/projects/mts/test.py | 55 +-
src/projects/mts/visualization.hpp | 4 +-
src/projects/online_vis/debruijn_environment.hpp | 2 +-
.../drawing_commands/draw_missasemblies.hpp | 6 +-
.../draw_part_of_genome_command.hpp | 2 +-
.../drawing_commands/draw_polymorphic_regions.hpp | 4 +-
.../drawing_commands/draw_poorly_assembled.hpp | 6 +-
src/projects/online_vis/errors.hpp | 2 +-
src/projects/online_vis/main.cpp | 14 +-
src/projects/online_vis/online_visualizer.hpp | 6 +-
src/projects/online_vis/setting_commands.hpp | 2 +-
src/projects/scaffold_correction/main.cpp | 20 +-
.../scaffold_correction/scaffold_correction.hpp | 8 +-
src/projects/spades/CMakeLists.txt | 1 +
src/projects/spades/chromosome_removal.cpp | 25 +-
src/projects/spades/chromosome_removal.hpp | 1 -
src/projects/spades/contig_output_stage.cpp | 82 +-
src/projects/spades/contig_output_stage.hpp | 15 +-
src/projects/spades/distance_estimation.cpp | 22 +-
src/projects/spades/gap_closer.cpp | 2 -
src/projects/spades/gap_closing.hpp | 42 +-
src/projects/spades/hybrid_aligning.cpp | 4 +-
src/projects/spades/hybrid_gap_closer.hpp | 174 +-
src/projects/spades/launch.hpp | 11 +-
src/projects/spades/main.cpp | 19 +-
src/projects/spades/pair_info_count.cpp | 145 +-
src/projects/spades/repeat_resolving.cpp | 1 +
src/projects/spades/second_phase_setup.cpp | 4 +-
src/projects/spades/second_phase_setup.hpp | 7 +-
.../{series_analysis.hpp => series_analysis.cpp} | 248 ++-
src/projects/spades/series_analysis.hpp | 306 +--
.../truseq_analysis/AlignmentAnalyserNew.cpp | 1 -
.../truseq_analysis/consistent_mapping.cpp | 3 +-
src/projects/truseq_analysis/consistent_mapping.h | 12 +-
src/projects/truseq_analysis/main.cpp | 16 +-
src/spades_pipeline/CMakeLists.txt | 2 +-
src/spades_pipeline/common/SeqIO.py | 34 +-
.../scripts => spades_pipeline/common}/__init__.py | 0
src/spades_pipeline/corrector_logic.py | 5 +-
src/spades_pipeline/hammer_logic.py | 9 +-
src/spades_pipeline/options_storage.py | 48 +-
src/spades_pipeline/spades_logic.py | 41 +-
src/spades_pipeline/support.py | 64 +-
test_dataset/reference_1K.fa.gz | Bin 534 -> 534 bytes
458 files changed, 20300 insertions(+), 14623 deletions(-)
create mode 100644 configs/corrector/log.properties
copy configs/debruijn/{careful_mode.info => careful_mda_mode.info} (64%)
create mode 100644 configs/debruijn/rna_fast_mode.info
create mode 100644 configs/debruijn/toy.info
create mode 100644 configs/debruijn/toy.yaml
delete mode 100644 ext/include/ConsensusCore/Feature.hpp
delete mode 100644 ext/include/ConsensusCore/Features.hpp
create mode 100644 ext/include/boomphf/BooPHF.h
create mode 100644 ext/include/llvm/Support/TrailingObjects.h
delete mode 100644 ext/src/ConsensusCore/Feature.cpp
delete mode 100644 ext/src/ConsensusCore/Features.cpp
delete mode 100644 src/common/adt/kmer_hash_vector.hpp
delete mode 100644 src/common/adt/parallel_seq_vector.hpp
delete mode 100644 src/common/adt/parallel_unordered_map.hpp
rename src/common/{utils/debruijn_graph =>
assembly_graph/construction}/debruijn_graph_constructor.hpp (61%)
rename src/common/{utils/debruijn_graph =>
assembly_graph/construction}/early_simplification.hpp (97%)
rename src/common/{utils/indices =>
assembly_graph/index}/edge_index_builders.hpp (65%)
rename src/common/{utils/indices =>
assembly_graph/index}/edge_info_updater.hpp (97%)
rename src/common/{utils/indices => assembly_graph/index}/edge_multi_index.hpp
(91%)
rename src/common/{utils/indices =>
assembly_graph/index}/edge_position_index.hpp (88%)
create mode 100644
src/common/assembly_graph/paths/bidirectional_path_container.hpp
rename src/common/{utils => math}/log.hpp (100%)
create mode 100644 src/common/modules/alignment/rna/ss_coverage.hpp
create mode 100644 src/common/modules/alignment/rna/ss_coverage_filler.hpp
copy src/common/{utils => modules}/coverage_model/CMakeLists.txt (100%)
rename src/common/{utils => modules}/coverage_model/kmer_coverage_model.cpp
(99%)
rename src/common/{utils => modules}/coverage_model/kmer_coverage_model.hpp
(98%)
rename src/common/{utils/coverage_model => paired_info}/CMakeLists.txt (67%)
create mode 100644 src/common/paired_info/distance_estimation.cpp
create mode 100644 src/common/paired_info/smoothing_distance_estimation.cpp
create mode 100644 src/common/paired_info/weighted_distance_estimation.cpp
rename src/common/{utils => sequence}/levenshtein.hpp (96%)
rename src/common/{utils => sequence}/range.hpp (95%)
rename src/common/utils/{indices => extension_index}/kmer_extension_index.hpp
(89%)
rename src/common/utils/{indices =>
extension_index}/kmer_extension_index_builder.hpp (95%)
rename src/common/utils/{ => filesystem}/copy_file.cpp (87%)
rename src/common/utils/{ => filesystem}/copy_file.hpp (63%)
rename src/common/utils/{ => filesystem}/file_limit.hpp (97%)
rename src/common/utils/{ => filesystem}/path_helper.cpp (97%)
rename src/common/utils/{ => filesystem}/path_helper.hpp (84%)
delete mode 100644 src/common/utils/indices/editable_index.hpp
delete mode 100644 src/common/utils/indices/kmer_splitters.hpp
rename configs/debruijn/simplification.info.template =>
src/common/utils/kmer_mph/1.cpp (100%)
rename src/common/utils/{mph_index => kmer_mph}/CMakeLists.txt (88%)
rename src/common/utils/{mph_index => kmer_mph}/kmer_index.hpp (80%)
rename src/common/utils/{mph_index => kmer_mph}/kmer_index_builder.hpp (57%)
rename src/common/utils/{mph_index => kmer_mph}/kmer_index_traits.hpp (76%)
create mode 100644 src/common/utils/kmer_mph/kmer_splitters.hpp
delete mode 100644 src/common/utils/mph_index/base_hash.hpp
delete mode 100644 src/common/utils/mph_index/bitpair_vector.cpp
delete mode 100644 src/common/utils/mph_index/bitpair_vector.hpp
delete mode 100644 src/common/utils/mph_index/common.hpp
delete mode 100644 src/common/utils/mph_index/emphf_config.hpp
delete mode 100644 src/common/utils/mph_index/hypergraph.hpp
delete mode 100644 src/common/utils/mph_index/hypergraph_sorter_seq.hpp
delete mode 100644 src/common/utils/mph_index/mphf.hpp
delete mode 100644 src/common/utils/mph_index/ranked_bitpair_vector.hpp
rename src/common/utils/{ => parallel}/openmp_wrapper.h (100%)
rename src/common/utils/{ => parallel}/parallel_wrapper.hpp (100%)
rename src/common/utils/{ => perf}/memory.hpp (91%)
rename src/common/utils/{ => perf}/memory_limit.hpp (97%)
rename src/common/utils/{ => perf}/perfcounter.hpp (64%)
rename src/common/utils/{indices => ph_map}/key_with_hash.hpp (99%)
rename src/common/utils/{indices => ph_map}/perfect_hash_map.hpp (97%)
rename src/common/utils/{indices => ph_map}/perfect_hash_map_builder.hpp (87%)
rename src/common/utils/{indices => ph_map}/storing_traits.hpp (83%)
rename src/common/utils/{indices => ph_map}/values.hpp (98%)
delete mode 100644 src/common/utils/simple_tools.hpp
create mode 100644 src/common/utils/stl_utils.hpp
delete mode 100644 src/projects/cclean/CMakeLists.txt
delete mode 100644 src/projects/cclean/adapter_index.cpp
delete mode 100644 src/projects/cclean/adapter_index.hpp
delete mode 100644 src/projects/cclean/additional.cpp
delete mode 100644 src/projects/cclean/brute_force_clean.cpp
delete mode 100644 src/projects/cclean/brute_force_clean.hpp
delete mode 100644 src/projects/cclean/comparator.hpp
delete mode 100644 src/projects/cclean/config_struct_cclean.cpp
delete mode 100644 src/projects/cclean/config_struct_cclean.hpp
delete mode 100644 src/projects/cclean/job_wrappers.cpp
delete mode 100644 src/projects/cclean/job_wrappers.hpp
delete mode 100644 src/projects/cclean/main.cpp
delete mode 100644 src/projects/cclean/output.cpp
delete mode 100644 src/projects/cclean/output.hpp
delete mode 100644 src/projects/cclean/running_modes.cpp
delete mode 100644 src/projects/cclean/running_modes.hpp
delete mode 100644 src/projects/cclean/utils.cpp
delete mode 100644 src/projects/cclean/utils.hpp
delete mode 100644 src/projects/cclean/valid_kmer_generator.hpp
create mode 100755 src/projects/ionhammer/comparator.py
delete mode 100644 src/projects/ionhammer/expander.cpp
delete mode 100644 src/projects/ionhammer/expander.hpp
create mode 100644 src/projects/ionhammer/gamma_poisson_model.cpp
create mode 100644 src/projects/ionhammer/gamma_poisson_model.hpp
delete mode 100644 src/projects/ionhammer/hamcluster.cpp
delete mode 100644 src/projects/ionhammer/hamcluster.hpp
create mode 100644 src/projects/ionhammer/hamcluster_1.cpp
create mode 100644 src/projects/ionhammer/hamcluster_1.h
create mode 100644 src/projects/ionhammer/io_read_corrector.hpp
create mode 100644 src/projects/ionhammer/kmer_evaluator.cpp
create mode 100644 src/projects/ionhammer/kmer_helpers.cpp
create mode 100644 src/projects/ionhammer/kmer_helpers.h
create mode 100644 src/projects/ionhammer/normal_quality_model.cpp
create mode 100644 src/projects/ionhammer/normal_quality_model.hpp
create mode 100644 src/projects/ionhammer/penalty_estimator.hpp
create mode 100644 src/projects/ionhammer/quality_metrics.cpp
create mode 100644 src/projects/ionhammer/quality_metrics.h
create mode 100644 src/projects/ionhammer/quality_thresholds_estimator.cpp
create mode 100644 src/projects/ionhammer/quality_thresholds_estimator.h
create mode 100644 src/projects/ionhammer/read_corrector_new.hpp
create mode 100644 src/projects/ionhammer/read_corrector_structs_new.h
create mode 100644 src/projects/ionhammer/reference.cpp
create mode 100644 src/projects/ionhammer/reference.h
create mode 100644 src/projects/ionhammer/thread_utils.h
create mode 100644 src/projects/mts/Reassembly.snake
copy src/projects/{hammer/quake_correct => mts/gzstream}/gzstream.C (98%)
copy src/projects/{hammer/quake_correct => mts/gzstream}/gzstream.h (93%)
create mode 100755 src/projects/mts/multirun.py
create mode 100644 src/projects/mts/scripts/Dataset_analysis.ipynb
create mode 100755 src/projects/mts/scripts/bhtsne.py
create mode 100755 src/projects/mts/scripts/bin_profiles.py
delete mode 100755 src/projects/mts/scripts/calc_kmers_mpl.py
delete mode 100755 src/projects/mts/scripts/canopy_launch.sh
create mode 100755 src/projects/mts/scripts/choose_bins.py
create mode 100755 src/projects/mts/scripts/clusters2csv.py
create mode 100755 src/projects/mts/scripts/contig_name_filter.py
create mode 100755 src/projects/mts/scripts/convert_output.py
create mode 100755 src/projects/mts/scripts/cut_fasta.py
create mode 100755 src/projects/mts/scripts/filter_bin.py
delete mode 100755 src/projects/mts/scripts/make_points_matrix.py
delete mode 100755 src/projects/mts/scripts/parse_output.py
delete mode 100755 src/projects/mts/scripts/ref_stats.sh
create mode 100755 src/projects/mts/scripts/run_tsne.py
create mode 100755 src/projects/mts/scripts/validate.pl
copy src/projects/spades/{series_analysis.hpp => series_analysis.cpp} (50%)
copy src/{projects/mts/scripts => spades_pipeline/common}/__init__.py (100%)
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