[med-svn] [spades] 03/05: Merge tag 'upstream/3.10.1+dfsg'
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed Apr 19 13:24:38 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a commit to branch master
in repository spades.
commit 7f5afdbd5b5c795862d0062c7de204ad7d92564d
Merge: ec8ce0a 34bcf2c
Author: Michael R. Crusoe <michael.crusoe at gmail.com>
Date: Wed Apr 19 02:55:47 2017 -0700
Merge tag 'upstream/3.10.1+dfsg'
Upstream version 3.10.1+dfsg
LICENSE | 2 +-
VERSION | 2 +-
changelog.html | 27 +
configs/debruijn/config.info | 32 +-
configs/debruijn/distance_estimation.info | 12 +-
configs/debruijn/large_genome_mode.info | 22 +
configs/debruijn/log.properties | 6 +
configs/debruijn/mda_mode.info | 11 +-
configs/debruijn/meta_mode.info | 49 +-
configs/debruijn/moleculo_mode.info | 2 +
configs/debruijn/path_extend/pe_params.info | 206 --
configs/debruijn/pe_params.info | 56 +-
configs/debruijn/rna_mode.info | 31 +-
configs/debruijn/simplification.info | 1 +
ext/include/btree/btree.h | 138 +-
ext/include/btree/btree_container.h | 45 +-
ext/include/btree/btree_map.h | 9 +
ext/include/btree/safe_btree.h | 32 +-
ext/include/btree/safe_btree_map.h | 8 +
ext/include/bwa/bntseq.h | 91 +
ext/include/bwa/bwa.h | 62 +
ext/include/bwa/bwamem.h | 184 ++
ext/include/bwa/bwt.h | 130 +
ext/include/bwa/utils.h | 111 +
ext/include/cuckoo/LICENSE | 18 +
ext/include/cuckoo/city_hasher.hh | 44 +
ext/include/cuckoo/cuckoohash_config.hh | 36 +
ext/include/cuckoo/cuckoohash_map.hh | 2537 ++++++++++++++++++++
ext/include/cuckoo/cuckoohash_util.hh | 136 ++
ext/include/cuckoo/libcuckoo_lazy_array.hh | 202 ++
ext/include/llvm/Support/MathExtras.h | 1 +
ext/src/CMakeLists.txt | 4 +-
ext/src/getopt_pp/CMakeLists.txt | 5 +
ext/{include => src}/getopt_pp/getopt_pp.cpp | 2 +-
ext/src/llvm/CMakeLists.txt | 3 +
manual.html | 105 +-
metaspades.py | 102 +-
plasmidspades.py | 102 +-
rnaspades.py | 102 +-
rnaspades_manual.html | 21 +-
spades.py | 102 +-
spades_compile.sh | 2 +-
src/CMakeLists.txt | 6 +-
src/cmake/options.cmake | 3 +
src/cmake/pack.cmake | 4 +-
src/common/CMakeLists.txt | 22 +
src/{utils => common}/adt/array_vector.hpp | 0
src/{utils => common}/adt/bag.hpp | 2 +-
src/{utils => common}/adt/bf.hpp | 0
src/{utils => common}/adt/chained_iterator.hpp | 0
src/{utils => common}/adt/concurrent_dsu.hpp | 2 +-
src/{utils => common}/adt/filter_iterator.hpp | 0
src/{utils => common}/adt/flat_map.hpp | 0
src/{utils => common}/adt/flat_set.hpp | 0
src/{utils => common}/adt/hll.hpp | 0
src/{utils => common}/adt/iterator_range.hpp | 0
src/{utils => common}/adt/kmer_hash_vector.hpp | 2 +-
src/{utils => common}/adt/kmer_vector.hpp | 17 +-
src/common/adt/loser_tree.hpp | 134 ++
src/{utils => common}/adt/parallel_seq_vector.hpp | 8 +-
.../adt/parallel_unordered_map.hpp | 0
src/{utils => common}/adt/pointer_iterator.hpp | 0
src/{utils => common}/adt/queue_iterator.hpp | 2 +-
src/{utils => common}/adt/small_pod_vector.hpp | 0
.../assembly_graph/CMakeLists.txt | 8 +-
.../components/component_filters.hpp | 0
.../components/connected_component.cpp | 0
.../components/connected_component.hpp | 2 +-
.../assembly_graph/components/graph_component.hpp | 226 ++
.../assembly_graph/components/splitters.hpp | 369 ++-
.../assembly_graph/core}/action_handlers.hpp | 4 +-
.../assembly_graph/core}/basic_graph_stats.hpp | 2 +-
.../assembly_graph/core}/construction_helper.hpp | 2 +-
.../assembly_graph/core}/coverage.hpp | 10 +-
.../assembly_graph/core}/debruijn_data.hpp | 8 +-
.../assembly_graph/core}/directions.hpp | 0
.../assembly_graph/core}/graph.hpp | 0
.../assembly_graph/core}/graph_core.hpp | 8 +-
.../assembly_graph/core}/graph_iterators.hpp | 14 +-
.../assembly_graph/core}/observable_graph.hpp | 2 +-
.../assembly_graph/core}/order_and_law.hpp | 4 +-
.../dijkstra/dijkstra_algorithm.hpp | 2 +-
.../assembly_graph}/dijkstra/dijkstra_helper.hpp | 10 +-
.../assembly_graph}/dijkstra/dijkstra_settings.hpp | 0
.../assembly_graph}/dijkstra/length_calculator.hpp | 2 +-
.../dijkstra/neighbours_iterator.hpp | 0
.../dijkstra/vertex_process_checker.hpp | 0
.../dijkstra/vertex_put_checker.hpp | 0
.../graph_support/basic_edge_conditions.hpp | 151 ++
.../graph_support/basic_vertex_conditions.hpp | 22 +-
.../assembly_graph/graph_support/chimera_stats.hpp | 0
.../assembly_graph/graph_support/comparators.hpp | 0
.../assembly_graph/graph_support/contig_output.hpp | 181 +-
.../graph_support/coverage_filling.hpp | 80 +
.../graph_support/coverage_uniformity_analyzer.cpp | 70 +
.../graph_support/coverage_uniformity_analyzer.hpp | 23 +
.../graph_support/detail_coverage.hpp | 88 +-
.../assembly_graph/graph_support/edge_removal.hpp | 172 ++
.../graph_support/genomic_quality.hpp | 37 +-
.../graph_support/graph_processing_algorithm.hpp | 146 ++
.../graph_support/marks_and_locks.hpp | 0
.../graph_support/parallel_processing.hpp | 306 +++
.../graph_support/scaff_supplementary.cpp | 270 +++
.../graph_support/scaff_supplementary.hpp | 100 +
.../handlers/edge_labels_handler.hpp | 2 +-
.../handlers/edges_position_handler.hpp | 5 +-
.../assembly_graph/handlers/id_track_handler.hpp | 4 +-
.../assembly_graph/paths/bidirectional_path.cpp | 2 +-
.../assembly_graph/paths/bidirectional_path.hpp | 42 +-
.../bidirectional_path_output.cpp | 68 +
.../bidirectional_path_output.hpp | 60 +
.../paths/bidirectional_path_io/io_support.cpp | 186 ++
.../paths/bidirectional_path_io/io_support.hpp | 190 ++
.../assembly_graph/paths/mapping_path.hpp | 79 +-
.../assembly_graph/paths/path_finders.hpp | 2 +-
.../assembly_graph/paths/path_processor.hpp | 147 +-
src/common/assembly_graph/paths/path_utils.hpp | 130 +
.../assembly_graph/stats/picture_dump.hpp | 94 +-
.../assembly_graph/stats/statistics.hpp | 2 +-
src/{modules => common}/empty.cpp | 0
.../pacbio_aligning.hpp => common/func/func.hpp} | 22 +-
src/{utils/adt => common/func}/function_traits.hpp | 9 +-
src/{modules/math => common/func}/pred.hpp | 54 +-
src/{modules => common}/io/CMakeLists.txt | 6 +-
src/common/io/dataset_support/dataset_readers.hpp | 121 +
.../io/dataset_support/read_converter.hpp | 96 +-
.../kmers_io => common/io/kmers}/kmer_iterator.hpp | 2 +-
.../io/kmers}/mmapped_reader.hpp | 6 +-
.../io/kmers}/mmapped_writer.hpp | 4 +-
.../io/reads}/binary_converter.hpp | 39 +-
src/common/io/reads/binary_streams.hpp | 140 ++
.../io/reads}/careful_filtering_reader_wrapper.hpp | 2 +-
.../io/reads}/converting_reader_wrapper.hpp | 0
.../io/reads}/delegating_reader_wrapper.hpp | 0
.../io/reads}/fasta_fastq_gz_parser.hpp | 10 +-
.../reads_io => common/io/reads}/file_reader.hpp | 4 +-
.../io/reads}/filtering_reader_wrapper.hpp | 0
.../io/reads_io => common/io/reads}/io_helper.hpp | 10 +-
.../io/reads_io => common/io/reads}/ireader.hpp | 2 +-
.../reads_io => common/io/reads}/ireadstream.hpp | 16 +-
.../io/reads}/modifying_reader_wrapper.hpp | 6 +-
.../reads_io => common/io/reads}/mpmc_bounded.hpp | 0
.../io/reads}/multifile_reader.hpp | 0
.../reads_io => common/io/reads}/orientation.hpp | 0
.../io/reads}/osequencestream.hpp | 35 +-
src/{modules => common}/io/reads/paired_read.hpp | 0
.../io/reads}/paired_readers.hpp | 2 +-
.../io/reads_io => common/io/reads}/parser.cpp | 10 +-
.../io/reads_io => common/io/reads}/parser.hpp | 2 +-
.../io/reads}/rc_reader_wrapper.hpp | 0
src/{modules => common}/io/reads/read.hpp | 12 +-
.../io/reads}/read_processor.hpp | 4 +-
.../io/reads}/read_stream_vector.hpp | 46 -
.../io/reads}/sequence_reader.hpp | 4 +-
src/{modules => common}/io/reads/single_read.hpp | 46 +-
.../io/reads}/splitting_wrapper.hpp | 10 +-
.../reads_io => common/io/reads}/vector_reader.hpp | 2 +-
.../io/reads}/wrapper_collection.hpp | 2 +-
.../io/sam_io => common/io/sam}/bam_parser.hpp | 10 +-
.../io/sam_io => common/io/sam}/bam_reader.hpp | 2 +-
src/{modules/io/sam_io => common/io/sam}/read.cpp | 2 +-
src/{modules/io/sam_io => common/io/sam}/read.hpp | 0
.../io/sam_io => common/io/sam}/sam_reader.cpp | 6 +-
.../io/sam_io => common/io/sam}/sam_reader.hpp | 2 +-
src/{modules => common}/math/smooth.hpp | 36 +-
src/{modules => common}/math/xmath.h | 0
.../algorithms => common/modules}/CMakeLists.txt | 6 +-
src/common/modules/alignment/bwa_index.cpp | 327 +++
src/common/modules/alignment/bwa_index.hpp | 44 +
.../modules/alignment/bwa_sequence_mapper.hpp | 35 +
.../modules/alignment}/edge_index.hpp | 10 +-
.../modules/alignment}/edge_index_refiller.cpp | 8 +-
.../modules/alignment}/edge_index_refiller.hpp | 0
.../modules/alignment}/kmer_map.hpp | 6 +-
.../modules/alignment}/kmer_mapper.hpp | 100 +-
.../modules/alignment}/kmer_mapper_logger.hpp | 6 +-
.../modules/alignment}/long_read_mapper.hpp | 126 +-
.../modules/alignment}/long_read_storage.hpp | 78 +-
.../modules/alignment}/pacbio/pac_index.hpp | 268 ++-
.../alignment}/pacbio/pacbio_read_structures.hpp | 121 +-
.../modules/alignment}/sequence_mapper.hpp | 130 +-
.../alignment}/sequence_mapper_notifier.hpp | 42 +-
.../modules/alignment}/short_read_mapper.hpp | 39 +-
.../modules}/genome_consistance_checker.cpp | 50 +-
.../modules}/genome_consistance_checker.hpp | 16 +-
.../modules}/graph_construction.hpp | 20 +-
.../modules}/graph_read_correction.hpp | 6 +-
.../modules}/mismatch_shall_not_pass.hpp | 32 +-
.../modules}/path_extend/CMakeLists.txt | 9 +-
.../modules}/path_extend/extension_chooser.hpp | 603 +----
.../modules}/path_extend/ideal_pair_info.hpp | 0
.../modules}/path_extend/loop_traverser.hpp | 76 +-
.../modules}/path_extend/overlap_analysis.hpp | 6 +-
.../modules}/path_extend/paired_library.hpp | 69 +-
.../modules}/path_extend/path_extender.hpp | 309 +--
.../modules}/path_extend/path_filter.hpp | 34 +-
.../modules}/path_extend/path_visualizer.hpp | 50 +-
.../modules}/path_extend/pe_config_struct.cpp | 58 +-
.../modules}/path_extend/pe_config_struct.hpp | 85 +-
.../modules}/path_extend/pe_resolver.hpp | 78 +-
.../modules}/path_extend/pe_utils.hpp | 167 +-
.../path_extend/pipeline/extenders_logic.cpp | 423 ++++
.../path_extend/pipeline/extenders_logic.hpp | 118 +
.../path_extend/pipeline/launch_support.cpp | 128 +
.../path_extend/pipeline/launch_support.hpp | 145 ++
.../modules/path_extend/pipeline/launcher.cpp | 448 ++++
.../modules/path_extend/pipeline/launcher.hpp | 115 +
.../scaffolder2015/connection_condition2015.cpp | 260 ++
.../scaffolder2015/connection_condition2015.hpp | 143 ++
.../scaffolder2015/extension_chooser2015.cpp | 37 +-
.../scaffolder2015/extension_chooser2015.hpp | 65 +
.../path_extend/scaffolder2015/path_polisher.cpp | 326 +++
.../path_extend/scaffolder2015/path_polisher.hpp | 85 +
.../path_extend/scaffolder2015/scaffold_graph.cpp | 31 +-
.../path_extend/scaffolder2015/scaffold_graph.hpp | 18 +-
.../scaffolder2015/scaffold_graph_constructor.cpp | 14 +-
.../scaffolder2015/scaffold_graph_constructor.hpp | 27 +-
.../scaffolder2015/scaffold_graph_visualizer.cpp | 23 +-
.../scaffolder2015/scaffold_graph_visualizer.hpp | 79 +
.../modules}/path_extend/split_graph_pair_info.hpp | 23 +-
src/common/modules/path_extend/weight_counter.hpp | 357 +++
.../modules}/simplification/bulge_remover.hpp | 153 +-
.../modules}/simplification/cleaner.hpp | 10 +-
.../simplification/complex_bulge_remover.hpp | 285 ++-
.../modules/simplification/complex_tip_clipper.hpp | 178 ++
.../modules}/simplification/compressor.hpp | 70 +-
.../simplification/dominated_set_finder.hpp | 3 +-
.../simplification/ec_threshold_finder.hpp | 6 +-
.../erroneous_connection_remover.hpp | 625 +++--
.../modules}/simplification/mf_ec_remover.hpp | 0
.../parallel_simplification_algorithms.hpp | 146 +-
.../simplification/relative_coverage_remover.hpp | 336 +--
.../modules}/simplification/tip_clipper.hpp | 39 +-
.../topological_edge_conditions.hpp} | 277 ++-
.../paired_info/concurrent_pair_info_buffer.hpp | 120 +
.../paired_info/data_divider.hpp | 2 +-
.../paired_info/distance_estimation.hpp | 49 +-
src/{modules => common}/paired_info/histogram.hpp | 21 +-
src/common/paired_info/histptr.hpp | 156 ++
.../paired_info/index_point.hpp | 0
.../paired_info/insert_size_refiner.hpp | 4 +-
src/{modules => common}/paired_info/is_counter.hpp | 71 +-
.../paired_info/pair_info_bounds.hpp | 2 +-
src/common/paired_info/pair_info_filler.hpp | 108 +
.../paired_info/pair_info_filters.hpp | 0
.../paired_info/pair_info_improver.hpp | 10 +-
.../paired_info/paired_info.hpp | 398 ++-
src/common/paired_info/paired_info_buffer.hpp | 227 ++
.../paired_info/paired_info_helpers.hpp | 0
.../paired_info/peak_finder.hpp | 2 +-
.../paired_info/smoothing_distance_estimation.hpp | 6 +-
.../paired_info/split_path_constructor.hpp | 18 +-
.../paired_info/weighted_distance_estimation.hpp | 38 +-
src/{modules => common}/paired_info/weights.hpp | 9 +-
src/{modules => common}/pipeline/CMakeLists.txt | 0
src/{modules => common}/pipeline/config_common.hpp | 6 +-
src/{modules => common}/pipeline/config_singl.hpp | 2 +-
src/{modules => common}/pipeline/config_struct.cpp | 65 +-
src/{modules => common}/pipeline/config_struct.hpp | 29 +-
src/{modules => common}/pipeline/genomic_info.hpp | 0
.../pipeline/genomic_info_filler.cpp | 6 +-
.../pipeline/genomic_info_filler.hpp | 0
src/{modules => common}/pipeline/graph_pack.hpp | 35 +-
src/{modules => common}/pipeline/graphio.hpp | 31 +-
src/{modules => common}/pipeline/library.cpp | 4 +-
src/{modules => common}/pipeline/library.hpp | 76 +-
src/{modules => common}/pipeline/library.inl | 0
src/{modules => common}/pipeline/stage.cpp | 2 +-
src/{modules => common}/pipeline/stage.hpp | 0
.../sequence/genome_storage.hpp} | 38 +-
.../data_structures => common}/sequence/nucl.hpp | 2 +-
.../sequence/quality.hpp | 0
.../data_structures => common}/sequence/rtseq.hpp | 21 +-
.../data_structures => common}/sequence/seq.hpp | 6 +-
.../sequence/seq_common.hpp} | 29 +-
.../sequence/sequence.hpp | 4 +-
.../sequence/sequence_tools.hpp | 4 +-
.../sequence/simple_seq.hpp | 6 +-
src/{modules => common}/stages/CMakeLists.txt | 0
src/{modules => common}/stages/construction.cpp | 8 +-
src/{modules => common}/stages/construction.hpp | 0
src/{modules => common}/stages/simplification.cpp | 253 +-
src/{modules => common}/stages/simplification.hpp | 0
.../graph_simplification.hpp | 678 ++++++
.../simplification_pipeline/rna_simplification.hpp | 22 +
.../simplification_settings.hpp | 2 +-
.../single_cell_simplification.hpp | 68 +-
src/{modules/math => common/utils}/CMakeLists.txt | 14 +-
.../utils}/autocompletion.cpp | 1 +
.../utils}/autocompletion.hpp | 0
.../dev_support => common/utils}/copy_file.cpp | 4 +-
.../dev_support => common/utils}/copy_file.hpp | 2 +-
.../utils/coverage_model}/CMakeLists.txt | 8 +-
.../utils/coverage_model}/kmer_coverage_model.cpp | 96 +-
.../utils/coverage_model}/kmer_coverage_model.hpp | 18 +-
.../dev_support => common/utils}/cpp_utils.hpp | 0
.../debruijn_graph/debruijn_graph_constructor.hpp | 56 +-
.../utils}/debruijn_graph/early_simplification.hpp | 13 +-
.../dev_support => common/utils}/file_limit.hpp | 2 +-
.../utils}/indices/edge_index_builders.hpp | 2 +-
.../utils}/indices/edge_info_updater.hpp | 51 +-
.../utils}/indices/edge_multi_index.hpp | 2 +-
.../utils}/indices/edge_position_index.hpp | 92 +-
.../utils}/indices/editable_index.hpp | 14 +-
.../utils}/indices/key_with_hash.hpp | 4 +-
.../utils}/indices/kmer_extension_index.hpp | 6 +-
.../indices/kmer_extension_index_builder.hpp | 14 +-
.../utils}/indices/kmer_splitters.hpp | 23 +-
.../utils}/indices/perfect_hash_map.hpp | 53 +-
.../utils}/indices/perfect_hash_map_builder.hpp | 10 +-
.../utils}/indices/storing_traits.hpp | 38 +-
.../utils}/indices/values.hpp | 0
src/{ => common}/utils/levenshtein.hpp | 2 +-
src/{modules/dev_support => common/utils}/log.hpp | 0
.../utils}/logger/log_writers.hpp | 2 +-
.../dev_support => common/utils}/logger/logger.hpp | 2 +-
.../utils}/logger/logger_impl.cpp | 2 +-
src/{modules/dev_support => common/utils}/md5.h | 0
.../dev_support => common/utils}/memory.hpp | 0
.../dev_support => common/utils}/memory_limit.hpp | 0
.../utils}/mph_index/CMakeLists.txt | 0
.../utils}/mph_index/base_hash.hpp | 0
.../utils}/mph_index/bitpair_vector.cpp | 0
.../utils}/mph_index/bitpair_vector.hpp | 0
.../utils}/mph_index/common.hpp | 0
.../utils}/mph_index/emphf_config.hpp | 0
.../utils}/mph_index/hypergraph.hpp | 0
.../utils}/mph_index/hypergraph_sorter_seq.hpp | 2 +-
.../utils}/mph_index/kmer_index.hpp | 0
.../utils}/mph_index/kmer_index_builder.hpp | 120 +-
.../utils}/mph_index/kmer_index_traits.hpp | 7 +-
.../utils}/mph_index/mphf.hpp | 2 +-
.../utils}/mph_index/ranked_bitpair_vector.hpp | 0
.../dev_support => common/utils}/openmp_wrapper.h | 0
.../utils}/parallel_wrapper.hpp | 0
.../dev_support => common/utils}/path_helper.cpp | 2 +-
.../dev_support => common/utils}/path_helper.hpp | 4 +-
.../dev_support => common/utils}/perfcounter.hpp | 0
.../dev_support => common/utils}/range.hpp | 2 +-
.../utils}/segfault_handler.hpp | 2 +-
.../dev_support => common/utils}/simple_tools.hpp | 13 +-
.../dev_support => common/utils}/stacktrace.hpp | 0
.../dev_support => common/utils}/standard_base.hpp | 10 +-
.../dev_support => common/utils}/verify.hpp | 2 +-
.../visualization/graph_colorer.hpp | 125 +-
.../visualization/graph_labeler.hpp | 94 +-
.../visualization}/graph_print_utils.hpp | 9 +-
.../visualization/graph_printer.hpp | 74 +-
.../visualization/position_filler.hpp | 47 +-
.../visualization/printing_parameter_storage.hpp | 21 +-
.../visualization/vertex_linker.hpp | 19 +-
.../visualization/visualization.hpp | 0
src/common/visualization/visualization_utils.hpp | 223 ++
.../visualization/visualizers.hpp | 97 +-
src/modules/CMakeLists.txt | 24 -
.../algorithms/path_extend/next_path_searcher.hpp | 1031 --------
.../algorithms/path_extend/path_extend_launch.hpp | 1257 ----------
src/modules/algorithms/path_extend/pe_io.hpp | 290 ---
.../scaffolder2015/connection_condition2015.cpp | 144 --
.../scaffolder2015/connection_condition2015.hpp | 90 -
.../scaffolder2015/extension_chooser2015.hpp | 59 -
.../scaffolder2015/scaffold_graph_visualizer.hpp | 73 -
.../algorithms/path_extend/weight_counter.hpp | 544 -----
.../simplification/complex_tip_clipper.hpp | 158 --
.../assembly_graph/components/graph_component.hpp | 198 --
.../graph_alignment/pacbio/pacbio_gap_closer.hpp | 396 ---
.../graph_support/graph_processing_algorithm.hpp | 262 --
.../graph_support/parallel_processing.hpp | 290 ---
.../graph_support/scaff_supplementary.cpp | 66 -
.../graph_support/scaff_supplementary.hpp | 77 -
src/modules/assembly_graph/paths/path_utils.hpp | 128 -
.../data_structures/sequence/CMakeLists.txt | 10 -
.../data_structures/sequence/genome_storage.hpp | 33 -
src/modules/dev_support/CMakeLists.txt | 13 -
src/modules/dev_support/func.hpp | 69 -
src/modules/io/dataset_support/dataset_readers.hpp | 122 -
src/modules/io/reads_io/binary_streams.hpp | 357 ---
src/modules/io/reads_io/cutting_reader_wrapper.hpp | 135 --
src/modules/io/reads_io/easy_reader.hpp | 122 -
src/modules/io/reads_io/is_corrupting_wrapper.hpp | 33 -
src/modules/paired_info/bwa_pair_info_filler.cpp | 408 ----
src/modules/paired_info/bwa_pair_info_filler.hpp | 253 --
src/modules/paired_info/pair_info_filler.hpp | 119 -
.../graph_simplification.hpp | 1034 --------
src/modules/visualization/visualization_utils.hpp | 210 --
src/projects/CMakeLists.txt | 2 +-
src/projects/cap/assembly_compare.hpp | 22 +-
src/projects/cap/assembly_problem_detection.hpp | 8 +-
src/projects/cap/cap_commands.hpp | 4 +-
src/projects/cap/cap_environment.hpp | 4 +-
src/projects/cap/cap_environment_manager.hpp | 2 +-
src/projects/cap/cap_kmer_index.hpp | 8 +-
src/projects/cap/cap_logger.hpp | 2 +-
src/projects/cap/colored_graph_construction.hpp | 10 +-
src/projects/cap/coloring.hpp | 25 +-
src/projects/cap/compare_standard.hpp | 26 +-
src/projects/cap/comparison_utils.hpp | 16 +-
src/projects/cap/coordinates_handler.hpp | 4 +-
src/projects/cap/deprecated/tools_deprecated.cpp | 4 +-
src/projects/cap/diff_masking.hpp | 10 +-
src/projects/cap/gene_analysis.hpp | 4 +-
src/projects/cap/genome_correction.hpp | 8 +-
src/projects/cap/junk_cropping_reader.hpp | 4 +-
src/projects/cap/longseq.hpp | 6 +-
src/projects/cap/main.cpp | 8 +-
src/projects/cap/mosaic.hpp | 20 +-
src/projects/cap/repeat_masking.hpp | 8 +-
src/projects/cap/serialization.hpp | 2 +-
src/projects/cap/simple_inversion_finder.hpp | 8 +-
src/projects/cap/stats.hpp | 38 +-
src/projects/cap/tools.cpp | 2 +-
src/projects/cap/untangling.hpp | 4 +-
src/projects/cap/visualization.hpp | 28 +-
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 +
.../cclean/comparator.hpp} | 20 +-
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 +
.../{hammer => cclean}/valid_kmer_generator.hpp | 32 +-
src/projects/corrector/CMakeLists.txt | 2 +-
src/projects/corrector/config_struct.cpp | 2 +-
src/projects/corrector/contig_processor.cpp | 8 +-
src/projects/corrector/contig_processor.hpp | 6 +-
src/projects/corrector/dataset_processor.cpp | 10 +-
src/projects/corrector/dataset_processor.hpp | 6 +-
.../corrector/interesting_pos_processor.cpp | 2 +-
src/projects/corrector/main.cpp | 4 +-
src/projects/dipspades/CMakeLists.txt | 6 +-
.../consensus_contigs_constructor.hpp | 4 +-
.../contig_correctors/close_gaps_corrector.hpp | 2 +-
src/projects/dipspades/dipspades.hpp | 4 +-
src/projects/dipspades/dipspades_config.cpp | 2 +-
.../conservative_regions_searcher.hpp | 4 +-
.../dipspades/kmer_gluing/equal_sequence_gluer.hpp | 2 +-
src/projects/dipspades/main.cpp | 10 +-
.../bulge_paths_searcher.hpp | 2 +-
.../complex_bulge_remover.hpp | 2 +-
.../polymorphic_bulge_remover.hpp | 8 +-
src/projects/dipspades/utils/edge_gluer.hpp | 2 +-
src/projects/dipspades/utils/path_routines.hpp | 5 +-
src/projects/hammer/CMakeLists.txt | 2 +-
src/projects/hammer/config_struct_hammer.cpp | 2 +-
src/projects/hammer/hamcluster.cpp | 4 +-
src/projects/hammer/hamcluster.hpp | 6 +-
src/projects/hammer/hammer_tools.cpp | 4 +-
src/projects/hammer/hammer_tools.hpp | 6 +-
src/projects/hammer/kmer_cluster.cpp | 4 +-
src/projects/hammer/kmer_data.cpp | 14 +-
src/projects/hammer/kmer_data.hpp | 4 +-
src/projects/hammer/kmer_stat.hpp | 4 +-
src/projects/hammer/main.cpp | 14 +-
src/projects/hammer/parallel_radix_sort.hpp | 2 +-
src/projects/hammer/quake_correct/bithash.cpp | 2 +-
src/projects/hammer/quake_count/quake_count.cpp | 2 +-
src/projects/hammer/quake_count/quake_count_17.cpp | 2 +-
src/projects/hammer/quake_count/quake_count_19.cpp | 2 +-
src/projects/hammer/quake_count/quake_count_21.cpp | 2 +-
src/projects/hammer/quake_count/quake_count_25.cpp | 2 +-
src/projects/hammer/quake_count/quake_count_29.cpp | 2 +-
src/projects/hammer/quake_count/quake_count_33.cpp | 2 +-
src/projects/hammer/quake_count/quake_count_37.cpp | 2 +-
src/projects/hammer/quake_count/quake_count_45.cpp | 2 +-
src/projects/hammer/quake_count/quake_count_55.cpp | 2 +-
src/projects/hammer/quake_count/quake_count_65.cpp | 2 +-
src/projects/hammer/quake_count/quake_count_75.cpp | 2 +-
.../hammer/quake_count/valid_kmer_generator.hpp | 2 +-
src/projects/hammer/quake_enhanced/count.cpp | 2 +-
src/projects/hammer/quake_enhanced/count/count.cpp | 2 +-
.../quake_enhanced/filter_trusted_enh/main.cpp | 2 +-
src/projects/hammer/valid_kmer_generator.hpp | 2 +-
src/projects/ionhammer/CMakeLists.txt | 2 +-
src/projects/ionhammer/HSeq.hpp | 2 +-
src/projects/ionhammer/config_struct.cpp | 2 +-
src/projects/ionhammer/err_helper_table.cpp | 2 +-
src/projects/ionhammer/err_helper_table.hpp | 2 +-
src/projects/ionhammer/expander.cpp | 2 +-
src/projects/ionhammer/hamcluster.cpp | 4 +-
src/projects/ionhammer/hamcluster.hpp | 4 +-
src/projects/ionhammer/kmer_data.cpp | 10 +-
src/projects/ionhammer/kmer_data.hpp | 2 +-
src/projects/ionhammer/main.cpp | 20 +-
src/projects/ionhammer/read_corrector.hpp | 2 +-
src/projects/ionhammer/subcluster.cpp | 2 +-
src/projects/mph_test/CMakeLists.txt | 2 +-
src/projects/mph_test/main.cpp | 27 +-
src/projects/mts/CMakeLists.txt | 57 +
src/projects/mts/Common.snake | 69 +
src/projects/mts/README | 21 +
src/projects/mts/Snakefile | 175 ++
src/projects/mts/Stats.snake | 270 +++
src/projects/mts/annotation.hpp | 310 +++
src/projects/mts/config.yaml | 10 +
src/projects/mts/contig_abundance.cpp | 176 ++
src/projects/mts/contig_abundance.hpp | 143 ++
src/projects/mts/contig_abundance_counter.cpp | 101 +
src/projects/mts/formats.hpp | 29 +
src/projects/mts/kmc_api/kmc_file.cpp | 1093 +++++++++
src/projects/mts/kmc_api/kmc_file.h | 141 ++
src/projects/mts/kmc_api/kmer_api.cpp | 48 +
src/projects/mts/kmc_api/kmer_api.h | 596 +++++
src/projects/mts/kmc_api/kmer_defs.h | 54 +
src/projects/mts/kmc_api/mmer.cpp | 49 +
src/projects/mts/kmc_api/mmer.h | 182 ++
src/projects/mts/kmc_api/stdafx.h | 4 +
src/projects/mts/kmer_multiplicity_counter.cpp | 256 ++
src/projects/mts/log.properties | 10 +
src/projects/mts/logger.hpp | 11 +
src/projects/mts/mts.py | 73 +
src/projects/mts/prop_binning.cpp | 128 +
src/projects/mts/propagate.cpp | 331 +++
src/projects/mts/propagate.hpp | 29 +
src/projects/mts/read_binning.cpp | 90 +
src/projects/mts/read_binning.hpp | 92 +
.../empty.cpp => projects/mts/scripts/__init__.py} | 0
src/projects/mts/scripts/calc_kmers_mpl.py | 38 +
src/projects/mts/scripts/canopy_launch.sh | 17 +
src/projects/mts/scripts/choose_samples.py | 61 +
src/projects/mts/scripts/combine_contigs.py | 28 +
src/projects/mts/scripts/common.py | 121 +
src/projects/mts/scripts/filter_nucmer.py | 54 +
src/projects/mts/scripts/gather_stats.py | 28 +
src/projects/mts/scripts/gen_samples.py | 96 +
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 | 77 +
src/projects/mts/scripts/ref_stats.sh | 63 +
src/projects/mts/scripts/split_bins.py | 30 +
src/projects/mts/stats.cpp | 194 ++
src/projects/mts/test.py | 205 ++
src/projects/mts/visualization.hpp | 66 +
src/projects/online_vis/CMakeLists.txt | 6 +-
src/projects/online_vis/debruijn_environment.hpp | 6 +-
.../drawing_commands/draw_contig_command.hpp | 2 +-
.../drawing_commands/draw_missasemblies.hpp | 4 +-
.../drawing_commands/draw_polymorphic_regions.hpp | 17 +-
.../drawing_commands/draw_poorly_assembled.hpp | 6 +-
.../drawing_commands/draw_position_command.hpp | 4 +-
.../drawing_commands/drawing_command.hpp | 8 +-
.../drawing_commands/show_position_command.hpp | 4 +-
src/projects/online_vis/environment.hpp | 6 +-
src/projects/online_vis/main.cpp | 10 +-
src/projects/online_vis/online_visualizer.hpp | 2 +-
.../position_commands/fill_position_command.hpp | 2 +-
src/projects/online_vis/processing_commands.hpp | 4 +-
src/projects/online_vis/standard_vis.hpp | 2 +-
.../junction_sequence_command.hpp | 4 +-
.../statistics_commands/print_contigs_stats.hpp | 2 +-
src/projects/online_vis/vis_logger.hpp | 6 +-
src/projects/scaffold_correction/CMakeLists.txt | 2 +-
src/projects/scaffold_correction/main.cpp | 15 +-
.../scaffold_correction/scaffold_correction.hpp | 17 +-
src/projects/spades/CMakeLists.txt | 10 +-
src/projects/spades/chromosome_removal.cpp | 45 +-
src/projects/spades/chromosome_removal.hpp | 3 +-
src/projects/spades/contig_output_stage.cpp | 55 +
src/projects/spades/contig_output_stage.hpp | 29 +
src/projects/spades/distance_estimation.cpp | 8 +-
src/projects/spades/gap_closer.cpp | 146 +-
src/projects/spades/gap_closing.hpp | 74 +
src/projects/spades/hybrid_aligning.cpp | 462 ++++
.../{pacbio_aligning.hpp => hybrid_aligning.hpp} | 6 +-
src/projects/spades/hybrid_gap_closer.hpp | 743 ++++++
src/projects/spades/launch.hpp | 69 +-
src/projects/spades/main.cpp | 8 +-
src/projects/spades/mismatch_correction.cpp | 4 +-
src/projects/spades/pacbio_aligning.cpp | 185 --
src/projects/spades/pair_info_count.cpp | 409 ++--
src/projects/spades/repeat_resolving.cpp | 60 +-
src/projects/spades/repeat_resolving.hpp | 12 -
src/projects/spades/second_phase_setup.cpp | 5 +-
src/projects/spades/second_phase_setup.hpp | 7 +-
src/projects/spades/series_analysis.hpp | 323 +++
.../truseq_analysis/AlignmentAnalyserNew.cpp | 4 +-
.../truseq_analysis/AlignmentAnalyserNew.hpp | 2 +-
src/projects/truseq_analysis/CMakeLists.txt | 2 +-
.../truseq_analysis/alignment_analyser.cpp | 2 +-
.../truseq_analysis/alignment_analyser.hpp | 4 +-
src/projects/truseq_analysis/analysis_pipeline.cpp | 6 +-
src/projects/truseq_analysis/analysis_pipeline.hpp | 2 +-
.../truseq_analysis/consistent_mapping.cpp | 2 +-
src/projects/truseq_analysis/main.cpp | 8 +-
src/spades_pipeline/corrector_logic.py | 6 +-
src/spades_pipeline/hammer_logic.py | 2 +
src/spades_pipeline/options_storage.py | 19 +-
src/spades_pipeline/spades_logic.py | 16 +-
src/spades_pipeline/support.py | 21 +
test_dataset_plasmid/pl1.fq.gz | Bin 0 -> 68202 bytes
test_dataset_plasmid/pl2.fq.gz | Bin 0 -> 68276 bytes
602 files changed, 25877 insertions(+), 13974 deletions(-)
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