[med-svn] [spades] branch master updated (bd3d481 -> 87072be)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed Apr 19 13:24:36 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch master
in repository spades.
from bd3d481 new Debian version
new ec8ce0a update copyright for new release
new 34bcf2c New upstream version 3.10.1+dfsg
new 7f5afdb Merge tag 'upstream/3.10.1+dfsg'
new cf27ea5 New upstream version 3.10.1
new 87072be spelling fixes
The 5 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
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 +
debian/changelog | 6 +
debian/control | 4 +-
debian/copyright | 67 +-
debian/patches/0003_accept-system-bwa.patch | 10 +-
.../0101_cmake_ignore_removed_python-yaml.patch | 11 +-
debian/patches/0103_use-debian-packaged-bwa.patch | 11 +-
debian/patches/0110_build_single_thread.patch | 6 +-
debian/patches/0111_use_full_config_dirs.patch | 8 +-
debian/patches/0112_spelling.patch | 78 -
debian/patches/0114_use_debian_provided_libs.patch | 185 +-
debian/patches/0115_enable_compiler_messages.patch | 6 +-
debian/patches/0116_stable_link_order.patch | 6 +-
debian/patches/0117_build_with_debug.patch | 8 +-
debian/patches/fix-bool-cast | 13 +
debian/patches/series | 2 +
debian/patches/spelling | 118 +
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/getopt_pp/getopt_pp.cpp | 206 --
ext/include/llvm/Support/MathExtras.h | 1 +
ext/src/CMakeLists.txt | 4 +-
ext/src/getopt_pp/CMakeLists.txt | 5 +
ext/src/getopt_pp/getopt_pp.cpp | 206 ++
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/common/adt/bag.hpp | 87 +
src/{utils => common}/adt/bf.hpp | 0
src/{utils => common}/adt/chained_iterator.hpp | 0
src/common/adt/concurrent_dsu.hpp | 297 +++
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/common/adt/kmer_hash_vector.hpp | 370 +++
src/common/adt/kmer_vector.hpp | 192 ++
src/common/adt/loser_tree.hpp | 134 ++
src/common/adt/parallel_seq_vector.hpp | 110 +
.../adt/parallel_unordered_map.hpp | 0
src/{utils => common}/adt/pointer_iterator.hpp | 0
src/common/adt/queue_iterator.hpp | 143 ++
src/{utils => common}/adt/small_pod_vector.hpp | 0
src/common/assembly_graph/CMakeLists.txt | 12 +
.../components/component_filters.hpp | 0
.../components/connected_component.cpp | 0
.../components/connected_component.hpp | 26 +
.../assembly_graph/components/graph_component.hpp | 226 ++
src/common/assembly_graph/components/splitters.hpp | 882 +++++++
src/common/assembly_graph/core/action_handlers.hpp | 347 +++
.../assembly_graph/core/basic_graph_stats.hpp | 53 +
.../assembly_graph/core/construction_helper.hpp | 84 +
src/common/assembly_graph/core/coverage.hpp | 335 +++
src/common/assembly_graph/core/debruijn_data.hpp | 170 ++
.../assembly_graph/core}/directions.hpp | 0
.../assembly_graph/core}/graph.hpp | 0
src/common/assembly_graph/core/graph_core.hpp | 620 +++++
src/common/assembly_graph/core/graph_iterators.hpp | 408 ++++
.../assembly_graph/core/observable_graph.hpp | 499 ++++
src/common/assembly_graph/core/order_and_law.hpp | 644 +++++
.../assembly_graph/dijkstra/dijkstra_algorithm.hpp | 288 +++
.../assembly_graph/dijkstra/dijkstra_helper.hpp | 163 ++
.../assembly_graph}/dijkstra/dijkstra_settings.hpp | 0
.../assembly_graph/dijkstra/length_calculator.hpp | 112 +
.../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 | 66 +
.../assembly_graph/graph_support/chimera_stats.hpp | 0
.../assembly_graph/graph_support/comparators.hpp | 0
.../assembly_graph/graph_support/contig_output.hpp | 602 +++++
.../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 | 190 ++
.../assembly_graph/graph_support/edge_removal.hpp | 172 ++
.../graph_support/genomic_quality.hpp | 555 +++++
.../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 | 226 ++
.../handlers/edges_position_handler.hpp | 212 ++
.../assembly_graph/handlers/id_track_handler.hpp | 110 +
.../assembly_graph/paths/bidirectional_path.cpp | 21 +
.../assembly_graph/paths/bidirectional_path.hpp | 1091 +++++++++
.../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 ++
src/common/assembly_graph/paths/mapping_path.hpp | 301 +++
src/common/assembly_graph/paths/path_finders.hpp | 124 +
src/common/assembly_graph/paths/path_processor.hpp | 386 +++
src/common/assembly_graph/paths/path_utils.hpp | 130 +
src/common/assembly_graph/stats/picture_dump.hpp | 455 ++++
src/common/assembly_graph/stats/statistics.hpp | 273 +++
src/{modules => common}/empty.cpp | 0
src/common/func/func.hpp | 25 +
src/common/func/function_traits.hpp | 71 +
src/common/func/pred.hpp | 175 ++
src/common/io/CMakeLists.txt | 16 +
src/common/io/dataset_support/dataset_readers.hpp | 121 +
src/common/io/dataset_support/read_converter.hpp | 279 +++
src/common/io/kmers/kmer_iterator.hpp | 54 +
src/common/io/kmers/mmapped_reader.hpp | 396 +++
src/common/io/kmers/mmapped_writer.hpp | 191 ++
src/common/io/reads/binary_converter.hpp | 262 ++
src/common/io/reads/binary_streams.hpp | 140 ++
.../io/reads/careful_filtering_reader_wrapper.hpp | 183 ++
.../io/reads}/converting_reader_wrapper.hpp | 0
.../io/reads}/delegating_reader_wrapper.hpp | 0
src/common/io/reads/fasta_fastq_gz_parser.hpp | 165 ++
src/common/io/reads/file_reader.hpp | 129 +
.../io/reads}/filtering_reader_wrapper.hpp | 0
src/common/io/reads/io_helper.hpp | 112 +
src/common/io/reads/ireader.hpp | 117 +
src/common/io/reads/ireadstream.hpp | 168 ++
src/common/io/reads/modifying_reader_wrapper.hpp | 115 +
.../reads_io => common/io/reads}/mpmc_bounded.hpp | 0
.../io/reads}/multifile_reader.hpp | 0
.../reads_io => common/io/reads}/orientation.hpp | 0
src/common/io/reads/osequencestream.hpp | 381 +++
src/{modules => common}/io/reads/paired_read.hpp | 0
src/common/io/reads/paired_readers.hpp | 252 ++
src/common/io/reads/parser.cpp | 90 +
src/common/io/reads/parser.hpp | 145 ++
.../io/reads}/rc_reader_wrapper.hpp | 0
src/common/io/reads/read.hpp | 244 ++
src/common/io/reads/read_processor.hpp | 209 ++
src/common/io/reads/read_stream_vector.hpp | 137 ++
src/common/io/reads/sequence_reader.hpp | 77 +
src/common/io/reads/single_read.hpp | 336 +++
src/common/io/reads/splitting_wrapper.hpp | 76 +
src/common/io/reads/vector_reader.hpp | 61 +
src/common/io/reads/wrapper_collection.hpp | 115 +
src/common/io/sam/bam_parser.hpp | 67 +
src/common/io/sam/bam_reader.hpp | 107 +
src/common/io/sam/read.cpp | 42 +
src/{modules/io/sam_io => common/io/sam}/read.hpp | 0
src/common/io/sam/sam_reader.cpp | 73 +
src/common/io/sam/sam_reader.hpp | 49 +
src/common/math/smooth.hpp | 189 ++
src/{modules => common}/math/xmath.h | 0
src/common/modules/CMakeLists.txt | 13 +
src/common/modules/alignment/bwa_index.cpp | 327 +++
src/common/modules/alignment/bwa_index.hpp | 44 +
.../modules/alignment/bwa_sequence_mapper.hpp | 35 +
src/common/modules/alignment/edge_index.hpp | 103 +
.../modules/alignment/edge_index_refiller.cpp | 33 +
.../modules/alignment}/edge_index_refiller.hpp | 0
src/common/modules/alignment/kmer_map.hpp | 151 ++
src/common/modules/alignment/kmer_mapper.hpp | 219 ++
.../modules/alignment/kmer_mapper_logger.hpp | 45 +
src/common/modules/alignment/long_read_mapper.hpp | 172 ++
src/common/modules/alignment/long_read_storage.hpp | 354 +++
src/common/modules/alignment/pacbio/pac_index.hpp | 916 +++++++
.../alignment/pacbio/pacbio_read_structures.hpp | 309 +++
src/common/modules/alignment/sequence_mapper.hpp | 405 ++++
.../modules/alignment/sequence_mapper_notifier.hpp | 184 ++
src/common/modules/alignment/short_read_mapper.hpp | 93 +
src/common/modules/genome_consistance_checker.cpp | 276 +++
src/common/modules/genome_consistance_checker.hpp | 79 +
src/common/modules/graph_construction.hpp | 180 ++
src/common/modules/graph_read_correction.hpp | 187 ++
src/common/modules/mismatch_shall_not_pass.hpp | 333 +++
src/common/modules/path_extend/CMakeLists.txt | 23 +
.../modules/path_extend/extension_chooser.hpp | 1162 +++++++++
.../modules}/path_extend/ideal_pair_info.hpp | 0
src/common/modules/path_extend/loop_traverser.hpp | 228 ++
.../modules/path_extend/overlap_analysis.hpp | 123 +
src/common/modules/path_extend/paired_library.hpp | 186 ++
src/common/modules/path_extend/path_extender.hpp | 1576 ++++++++++++
src/common/modules/path_extend/path_filter.hpp | 186 ++
src/common/modules/path_extend/path_visualizer.hpp | 172 ++
.../modules/path_extend/pe_config_struct.cpp | 211 ++
.../modules/path_extend/pe_config_struct.hpp | 246 ++
src/common/modules/path_extend/pe_resolver.hpp | 577 +++++
src/common/modules/path_extend/pe_utils.hpp | 397 +++
.../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 | 93 +
.../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 | 258 ++
.../path_extend/scaffolder2015/scaffold_graph.hpp | 228 ++
.../scaffolder2015/scaffold_graph_constructor.cpp | 75 +
.../scaffolder2015/scaffold_graph_constructor.hpp | 80 +
.../scaffolder2015/scaffold_graph_visualizer.cpp | 69 +
.../scaffolder2015/scaffold_graph_visualizer.hpp | 79 +
.../modules/path_extend/split_graph_pair_info.hpp | 432 ++++
src/common/modules/path_extend/weight_counter.hpp | 357 +++
.../modules/simplification/bulge_remover.hpp | 680 ++++++
src/common/modules/simplification/cleaner.hpp | 39 +
.../simplification/complex_bulge_remover.hpp | 1215 ++++++++++
.../modules/simplification/complex_tip_clipper.hpp | 178 ++
src/common/modules/simplification/compressor.hpp | 125 +
.../simplification/dominated_set_finder.hpp | 136 ++
.../modules/simplification/ec_threshold_finder.hpp | 152 ++
.../erroneous_connection_remover.hpp | 659 +++++
.../modules}/simplification/mf_ec_remover.hpp | 0
.../parallel_simplification_algorithms.hpp | 900 +++++++
.../simplification/relative_coverage_remover.hpp | 690 ++++++
src/common/modules/simplification/tip_clipper.hpp | 248 ++
.../simplification/topological_edge_conditions.hpp | 286 +++
.../paired_info/concurrent_pair_info_buffer.hpp | 120 +
src/common/paired_info/data_divider.hpp | 137 ++
src/common/paired_info/distance_estimation.hpp | 300 +++
src/common/paired_info/histogram.hpp | 199 ++
src/common/paired_info/histptr.hpp | 156 ++
.../paired_info/index_point.hpp | 0
src/common/paired_info/insert_size_refiner.hpp | 165 ++
src/common/paired_info/is_counter.hpp | 150 ++
src/common/paired_info/pair_info_bounds.hpp | 30 +
src/common/paired_info/pair_info_filler.hpp | 108 +
.../paired_info/pair_info_filters.hpp | 0
src/common/paired_info/pair_info_improver.hpp | 280 +++
src/common/paired_info/paired_info.hpp | 630 +++++
src/common/paired_info/paired_info_buffer.hpp | 227 ++
.../paired_info/paired_info_helpers.hpp | 0
src/common/paired_info/peak_finder.hpp | 385 +++
.../paired_info/smoothing_distance_estimation.hpp | 283 +++
src/common/paired_info/split_path_constructor.hpp | 142 ++
.../paired_info/weighted_distance_estimation.hpp | 112 +
src/common/paired_info/weights.hpp | 83 +
src/{modules => common}/pipeline/CMakeLists.txt | 0
src/common/pipeline/config_common.hpp | 140 ++
src/common/pipeline/config_singl.hpp | 57 +
src/common/pipeline/config_struct.cpp | 858 +++++++
src/common/pipeline/config_struct.hpp | 608 +++++
src/{modules => common}/pipeline/genomic_info.hpp | 0
src/common/pipeline/genomic_info_filler.cpp | 149 ++
.../pipeline/genomic_info_filler.hpp | 0
src/common/pipeline/graph_pack.hpp | 170 ++
src/common/pipeline/graphio.hpp | 1047 ++++++++
src/common/pipeline/library.cpp | 139 ++
src/common/pipeline/library.hpp | 368 +++
src/{modules => common}/pipeline/library.inl | 0
src/common/pipeline/stage.cpp | 133 +
src/{modules => common}/pipeline/stage.hpp | 0
src/common/sequence/genome_storage.hpp | 55 +
src/common/sequence/nucl.hpp | 123 +
.../sequence/quality.hpp | 0
src/common/sequence/rtseq.hpp | 751 ++++++
src/common/sequence/seq.hpp | 529 ++++
src/common/sequence/seq_common.hpp | 44 +
src/common/sequence/sequence.hpp | 553 +++++
src/common/sequence/sequence_tools.hpp | 159 ++
src/common/sequence/simple_seq.hpp | 157 ++
src/{modules => common}/stages/CMakeLists.txt | 0
src/common/stages/construction.cpp | 70 +
src/{modules => common}/stages/construction.hpp | 0
src/common/stages/simplification.cpp | 613 +++++
src/{modules => common}/stages/simplification.hpp | 0
.../graph_simplification.hpp | 678 ++++++
.../simplification_pipeline/rna_simplification.hpp | 22 +
.../simplification_settings.hpp | 112 +
.../single_cell_simplification.hpp | 142 ++
src/common/utils/CMakeLists.txt | 20 +
src/common/utils/autocompletion.cpp | 52 +
.../utils}/autocompletion.hpp | 0
src/common/utils/copy_file.cpp | 158 ++
src/common/utils/copy_file.hpp | 18 +
src/common/utils/coverage_model/CMakeLists.txt | 14 +
.../utils/coverage_model/kmer_coverage_model.cpp | 380 +++
.../utils/coverage_model/kmer_coverage_model.hpp | 48 +
.../dev_support => common/utils}/cpp_utils.hpp | 0
.../debruijn_graph/debruijn_graph_constructor.hpp | 558 +++++
.../utils/debruijn_graph/early_simplification.hpp | 191 ++
src/common/utils/file_limit.hpp | 33 +
src/common/utils/indices/edge_index_builders.hpp | 174 ++
src/common/utils/indices/edge_info_updater.hpp | 109 +
src/common/utils/indices/edge_multi_index.hpp | 155 ++
src/common/utils/indices/edge_position_index.hpp | 216 ++
src/common/utils/indices/editable_index.hpp | 270 +++
src/common/utils/indices/key_with_hash.hpp | 229 ++
src/common/utils/indices/kmer_extension_index.hpp | 309 +++
.../utils/indices/kmer_extension_index_builder.hpp | 106 +
src/common/utils/indices/kmer_splitters.hpp | 317 +++
src/common/utils/indices/perfect_hash_map.hpp | 339 +++
.../utils/indices/perfect_hash_map_builder.hpp | 102 +
src/common/utils/indices/storing_traits.hpp | 81 +
.../utils}/indices/values.hpp | 0
src/common/utils/levenshtein.hpp | 241 ++
src/{modules/dev_support => common/utils}/log.hpp | 0
src/common/utils/logger/log_writers.hpp | 43 +
src/common/utils/logger/logger.hpp | 149 ++
src/common/utils/logger/logger_impl.cpp | 148 ++
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 | 130 +
.../utils}/mph_index/kmer_index.hpp | 0
src/common/utils/mph_index/kmer_index_builder.hpp | 486 ++++
src/common/utils/mph_index/kmer_index_traits.hpp | 92 +
src/common/utils/mph_index/mphf.hpp | 136 ++
.../utils}/mph_index/ranked_bitpair_vector.hpp | 0
.../dev_support => common/utils}/openmp_wrapper.h | 0
.../utils}/parallel_wrapper.hpp | 0
src/common/utils/path_helper.cpp | 249 ++
src/common/utils/path_helper.hpp | 74 +
.../dev_support => common/utils}/perfcounter.hpp | 0
src/common/utils/range.hpp | 92 +
src/common/utils/segfault_handler.hpp | 58 +
src/common/utils/simple_tools.hpp | 189 ++
.../dev_support => common/utils}/stacktrace.hpp | 0
src/common/utils/standard_base.hpp | 140 ++
src/common/utils/verify.hpp | 33 +
src/common/visualization/graph_colorer.hpp | 355 +++
src/common/visualization/graph_labeler.hpp | 308 +++
src/common/visualization/graph_print_utils.hpp | 327 +++
src/common/visualization/graph_printer.hpp | 186 ++
src/common/visualization/position_filler.hpp | 96 +
.../visualization/printing_parameter_storage.hpp | 88 +
src/common/visualization/vertex_linker.hpp | 46 +
.../visualization/visualization.hpp | 0
src/common/visualization/visualization_utils.hpp | 223 ++
src/common/visualization/visualizers.hpp | 180 ++
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/length_calculator.hpp | 112 -
.../algorithms/genome_consistance_checker.cpp | 238 --
.../algorithms/genome_consistance_checker.hpp | 77 -
src/modules/algorithms/graph_construction.hpp | 180 --
src/modules/algorithms/graph_read_correction.hpp | 187 --
src/modules/algorithms/mismatch_shall_not_pass.hpp | 339 ---
src/modules/algorithms/path_extend/CMakeLists.txt | 18 -
.../algorithms/path_extend/extension_chooser.hpp | 1555 ------------
.../algorithms/path_extend/loop_traverser.hpp | 224 --
.../algorithms/path_extend/next_path_searcher.hpp | 1031 --------
.../algorithms/path_extend/overlap_analysis.hpp | 123 -
.../algorithms/path_extend/paired_library.hpp | 179 --
.../algorithms/path_extend/path_extend_launch.hpp | 1257 ----------
.../algorithms/path_extend/path_extender.hpp | 1561 ------------
src/modules/algorithms/path_extend/path_filter.hpp | 158 --
.../algorithms/path_extend/path_visualizer.hpp | 172 --
.../algorithms/path_extend/pe_config_struct.cpp | 199 --
.../algorithms/path_extend/pe_config_struct.hpp | 271 ---
src/modules/algorithms/path_extend/pe_io.hpp | 290 ---
src/modules/algorithms/path_extend/pe_resolver.hpp | 523 ----
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 | 59 -
.../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 | 101 -
.../scaffolder2015/scaffold_graph_visualizer.cpp | 72 -
.../scaffolder2015/scaffold_graph_visualizer.hpp | 73 -
.../path_extend/split_graph_pair_info.hpp | 449 ----
.../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 | 158 --
.../algorithms/simplification/compressor.hpp | 141 --
.../simplification/dominated_set_finder.hpp | 137 --
.../simplification/ec_threshold_finder.hpp | 152 --
.../erroneous_connection_remover.hpp | 690 ------
.../parallel_simplification_algorithms.hpp | 820 -------
.../simplification/relative_coverage_remover.hpp | 674 ------
.../algorithms/simplification/tip_clipper.hpp | 271 ---
src/modules/assembly_graph/CMakeLists.txt | 12 -
.../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 | 103 -
.../graph_alignment/edge_index_refiller.cpp | 33 -
.../assembly_graph/graph_alignment/kmer_map.hpp | 151 --
.../assembly_graph/graph_alignment/kmer_mapper.hpp | 239 --
.../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 | 824 -------
.../graph_alignment/pacbio/pacbio_gap_closer.hpp | 396 ---
.../pacbio/pacbio_read_structures.hpp | 320 ---
.../graph_alignment/sequence_mapper.hpp | 387 ---
.../graph_alignment/sequence_mapper_notifier.hpp | 178 --
.../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 | 84 -
src/modules/assembly_graph/graph_core/coverage.hpp | 343 ---
.../assembly_graph/graph_core/debruijn_data.hpp | 170 --
.../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 | 273 ---
.../graph_support/basic_vertex_conditions.hpp | 52 -
.../assembly_graph/graph_support/contig_output.hpp | 425 ----
.../graph_support/detail_coverage.hpp | 258 --
.../graph_support/genomic_quality.hpp | 554 -----
.../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 -
.../handlers/edge_labels_handler.hpp | 226 --
.../handlers/edges_position_handler.hpp | 213 --
.../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 | 232 --
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 | 447 ----
src/modules/assembly_graph/stats/statistics.hpp | 273 ---
.../debruijn_graph/debruijn_graph_constructor.hpp | 548 -----
.../debruijn_graph/early_simplification.hpp | 192 --
.../indices/edge_index_builders.hpp | 174 --
.../data_structures/indices/edge_info_updater.hpp | 108 -
.../data_structures/indices/edge_multi_index.hpp | 155 --
.../indices/edge_position_index.hpp | 184 --
.../data_structures/indices/editable_index.hpp | 270 ---
.../data_structures/indices/key_with_hash.hpp | 227 --
.../indices/kmer_extension_index.hpp | 309 ---
.../indices/kmer_extension_index_builder.hpp | 106 -
.../data_structures/indices/kmer_splitters.hpp | 312 ---
.../data_structures/indices/perfect_hash_map.hpp | 318 ---
.../indices/perfect_hash_map_builder.hpp | 102 -
.../data_structures/indices/storing_traits.hpp | 61 -
.../mph_index/hypergraph_sorter_seq.hpp | 130 -
.../mph_index/kmer_index_builder.hpp | 404 ----
.../mph_index/kmer_index_traits.hpp | 87 -
src/modules/data_structures/mph_index/mphf.hpp | 136 --
.../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/rtseq.hpp | 740 ------
src/modules/data_structures/sequence/runtime_k.hpp | 47 -
src/modules/data_structures/sequence/seq.hpp | 529 ----
.../data_structures/sequence/seq_common.hpp | 20 -
src/modules/data_structures/sequence/sequence.hpp | 553 -----
.../data_structures/sequence/sequence_tools.hpp | 159 --
.../data_structures/sequence/simple_seq.hpp | 157 --
src/modules/dev_support/CMakeLists.txt | 13 -
src/modules/dev_support/autocompletion.cpp | 51 -
src/modules/dev_support/copy_file.cpp | 158 --
src/modules/dev_support/copy_file.hpp | 18 -
src/modules/dev_support/file_limit.hpp | 33 -
src/modules/dev_support/func.hpp | 69 -
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/path_helper.cpp | 249 --
src/modules/dev_support/path_helper.hpp | 74 -
src/modules/dev_support/range.hpp | 92 -
src/modules/dev_support/segfault_handler.hpp | 58 -
src/modules/dev_support/simple_tools.hpp | 184 --
src/modules/dev_support/standard_base.hpp | 140 --
src/modules/dev_support/verify.hpp | 33 -
src/modules/io/CMakeLists.txt | 16 -
src/modules/io/dataset_support/dataset_readers.hpp | 122 -
src/modules/io/dataset_support/read_converter.hpp | 273 ---
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/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 --
src/modules/io/reads_io/cutting_reader_wrapper.hpp | 135 --
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 -
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 | 115 -
src/modules/io/reads_io/osequencestream.hpp | 374 ---
src/modules/io/reads_io/paired_readers.hpp | 252 --
src/modules/io/reads_io/parser.cpp | 90 -
src/modules/io/reads_io/parser.hpp | 145 --
src/modules/io/reads_io/read_processor.hpp | 209 --
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 | 76 -
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/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/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/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_improver.hpp | 280 ---
src/modules/paired_info/paired_info.hpp | 712 ------
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/config_common.hpp | 140 --
src/modules/pipeline/config_singl.hpp | 57 -
src/modules/pipeline/config_struct.cpp | 819 -------
src/modules/pipeline/config_struct.hpp | 583 -----
src/modules/pipeline/genomic_info_filler.cpp | 149 --
src/modules/pipeline/graph_pack.hpp | 161 --
src/modules/pipeline/graphio.hpp | 1040 --------
src/modules/pipeline/library.cpp | 137 --
src/modules/pipeline/library.hpp | 366 ---
src/modules/pipeline/stage.cpp | 133 -
src/modules/stages/construction.cpp | 70 -
src/modules/stages/simplification.cpp | 574 -----
.../graph_simplification.hpp | 1034 --------
.../simplification_settings.hpp | 112 -
.../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 | 93 -
.../visualization/printing_parameter_storage.hpp | 81 -
src/modules/visualization/vertex_linker.hpp | 41 -
src/modules/visualization/visualization_utils.hpp | 210 --
src/modules/visualization/visualizers.hpp | 173 --
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 +
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/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 +
.../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 ++++
src/projects/spades/hybrid_aligning.hpp | 23 +
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/pacbio_aligning.hpp | 23 -
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 +
src/utils/adt/bag.hpp | 87 -
src/utils/adt/concurrent_dsu.hpp | 297 ---
src/utils/adt/function_traits.hpp | 76 -
src/utils/adt/kmer_hash_vector.hpp | 370 ---
src/utils/adt/kmer_vector.hpp | 179 --
src/utils/adt/parallel_seq_vector.hpp | 110 -
src/utils/adt/queue_iterator.hpp | 143 --
src/utils/levenshtein.hpp | 241 --
test_dataset_plasmid/pl1.fq.gz | Bin 0 -> 68202 bytes
test_dataset_plasmid/pl2.fq.gz | Bin 0 -> 68276 bytes
817 files changed, 70805 insertions(+), 58590 deletions(-)
create mode 100644 configs/debruijn/large_genome_mode.info
delete mode 100644 configs/debruijn/path_extend/pe_params.info
delete mode 100644 debian/patches/0112_spelling.patch
create mode 100644 debian/patches/fix-bool-cast
create mode 100644 debian/patches/spelling
create mode 100644 ext/include/bwa/bntseq.h
create mode 100644 ext/include/bwa/bwa.h
create mode 100644 ext/include/bwa/bwamem.h
create mode 100644 ext/include/bwa/bwt.h
create mode 100644 ext/include/bwa/utils.h
create mode 100644 ext/include/cuckoo/LICENSE
create mode 100644 ext/include/cuckoo/city_hasher.hh
create mode 100644 ext/include/cuckoo/cuckoohash_config.hh
create mode 100644 ext/include/cuckoo/cuckoohash_map.hh
create mode 100644 ext/include/cuckoo/cuckoohash_util.hh
create mode 100644 ext/include/cuckoo/libcuckoo_lazy_array.hh
delete mode 100644 ext/include/getopt_pp/getopt_pp.cpp
create mode 100644 ext/src/getopt_pp/CMakeLists.txt
create mode 100644 ext/src/getopt_pp/getopt_pp.cpp
create mode 100644 src/common/CMakeLists.txt
rename src/{utils => common}/adt/array_vector.hpp (100%)
create mode 100644 src/common/adt/bag.hpp
rename src/{utils => common}/adt/bf.hpp (100%)
rename src/{utils => common}/adt/chained_iterator.hpp (100%)
create mode 100644 src/common/adt/concurrent_dsu.hpp
rename src/{utils => common}/adt/filter_iterator.hpp (100%)
rename src/{utils => common}/adt/flat_map.hpp (100%)
rename src/{utils => common}/adt/flat_set.hpp (100%)
rename src/{utils => common}/adt/hll.hpp (100%)
rename src/{utils => common}/adt/iterator_range.hpp (100%)
create mode 100644 src/common/adt/kmer_hash_vector.hpp
create mode 100644 src/common/adt/kmer_vector.hpp
create mode 100644 src/common/adt/loser_tree.hpp
create mode 100644 src/common/adt/parallel_seq_vector.hpp
rename src/{utils => common}/adt/parallel_unordered_map.hpp (100%)
rename src/{utils => common}/adt/pointer_iterator.hpp (100%)
create mode 100644 src/common/adt/queue_iterator.hpp
rename src/{utils => common}/adt/small_pod_vector.hpp (100%)
create mode 100644 src/common/assembly_graph/CMakeLists.txt
rename src/{modules => common}/assembly_graph/components/component_filters.hpp (100%)
rename src/{modules => common}/assembly_graph/components/connected_component.cpp (100%)
create mode 100644 src/common/assembly_graph/components/connected_component.hpp
create mode 100644 src/common/assembly_graph/components/graph_component.hpp
create mode 100644 src/common/assembly_graph/components/splitters.hpp
create mode 100644 src/common/assembly_graph/core/action_handlers.hpp
create mode 100644 src/common/assembly_graph/core/basic_graph_stats.hpp
create mode 100644 src/common/assembly_graph/core/construction_helper.hpp
create mode 100644 src/common/assembly_graph/core/coverage.hpp
create mode 100644 src/common/assembly_graph/core/debruijn_data.hpp
rename src/{modules/assembly_graph/graph_core => common/assembly_graph/core}/directions.hpp (100%)
rename src/{modules/assembly_graph/graph_core => common/assembly_graph/core}/graph.hpp (100%)
create mode 100644 src/common/assembly_graph/core/graph_core.hpp
create mode 100644 src/common/assembly_graph/core/graph_iterators.hpp
create mode 100644 src/common/assembly_graph/core/observable_graph.hpp
create mode 100644 src/common/assembly_graph/core/order_and_law.hpp
create mode 100644 src/common/assembly_graph/dijkstra/dijkstra_algorithm.hpp
create mode 100644 src/common/assembly_graph/dijkstra/dijkstra_helper.hpp
rename src/{modules/algorithms => common/assembly_graph}/dijkstra/dijkstra_settings.hpp (100%)
create mode 100644 src/common/assembly_graph/dijkstra/length_calculator.hpp
rename src/{modules/algorithms => common/assembly_graph}/dijkstra/neighbours_iterator.hpp (100%)
rename src/{modules/algorithms => common/assembly_graph}/dijkstra/vertex_process_checker.hpp (100%)
rename src/{modules/algorithms => common/assembly_graph}/dijkstra/vertex_put_checker.hpp (100%)
create mode 100644 src/common/assembly_graph/graph_support/basic_edge_conditions.hpp
create mode 100644 src/common/assembly_graph/graph_support/basic_vertex_conditions.hpp
rename src/{modules => common}/assembly_graph/graph_support/chimera_stats.hpp (100%)
rename src/{modules => common}/assembly_graph/graph_support/comparators.hpp (100%)
create mode 100644 src/common/assembly_graph/graph_support/contig_output.hpp
create mode 100644 src/common/assembly_graph/graph_support/coverage_filling.hpp
create mode 100644 src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.cpp
create mode 100644 src/common/assembly_graph/graph_support/coverage_uniformity_analyzer.hpp
create mode 100644 src/common/assembly_graph/graph_support/detail_coverage.hpp
create mode 100644 src/common/assembly_graph/graph_support/edge_removal.hpp
create mode 100644 src/common/assembly_graph/graph_support/genomic_quality.hpp
create mode 100644 src/common/assembly_graph/graph_support/graph_processing_algorithm.hpp
rename src/{modules => common}/assembly_graph/graph_support/marks_and_locks.hpp (100%)
create mode 100644 src/common/assembly_graph/graph_support/parallel_processing.hpp
create mode 100644 src/common/assembly_graph/graph_support/scaff_supplementary.cpp
create mode 100644 src/common/assembly_graph/graph_support/scaff_supplementary.hpp
create mode 100644 src/common/assembly_graph/handlers/edge_labels_handler.hpp
create mode 100644 src/common/assembly_graph/handlers/edges_position_handler.hpp
create mode 100644 src/common/assembly_graph/handlers/id_track_handler.hpp
create mode 100644 src/common/assembly_graph/paths/bidirectional_path.cpp
create mode 100644 src/common/assembly_graph/paths/bidirectional_path.hpp
create mode 100644 src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.cpp
create mode 100644 src/common/assembly_graph/paths/bidirectional_path_io/bidirectional_path_output.hpp
create mode 100644 src/common/assembly_graph/paths/bidirectional_path_io/io_support.cpp
create mode 100644 src/common/assembly_graph/paths/bidirectional_path_io/io_support.hpp
create mode 100644 src/common/assembly_graph/paths/mapping_path.hpp
create mode 100644 src/common/assembly_graph/paths/path_finders.hpp
create mode 100644 src/common/assembly_graph/paths/path_processor.hpp
create mode 100644 src/common/assembly_graph/paths/path_utils.hpp
create mode 100644 src/common/assembly_graph/stats/picture_dump.hpp
create mode 100644 src/common/assembly_graph/stats/statistics.hpp
rename src/{modules => common}/empty.cpp (100%)
create mode 100644 src/common/func/func.hpp
create mode 100644 src/common/func/function_traits.hpp
create mode 100644 src/common/func/pred.hpp
create mode 100644 src/common/io/CMakeLists.txt
create mode 100644 src/common/io/dataset_support/dataset_readers.hpp
create mode 100644 src/common/io/dataset_support/read_converter.hpp
create mode 100644 src/common/io/kmers/kmer_iterator.hpp
create mode 100644 src/common/io/kmers/mmapped_reader.hpp
create mode 100644 src/common/io/kmers/mmapped_writer.hpp
create mode 100644 src/common/io/reads/binary_converter.hpp
create mode 100644 src/common/io/reads/binary_streams.hpp
create mode 100644 src/common/io/reads/careful_filtering_reader_wrapper.hpp
rename src/{modules/io/reads_io => common/io/reads}/converting_reader_wrapper.hpp (100%)
rename src/{modules/io/reads_io => common/io/reads}/delegating_reader_wrapper.hpp (100%)
create mode 100644 src/common/io/reads/fasta_fastq_gz_parser.hpp
create mode 100644 src/common/io/reads/file_reader.hpp
rename src/{modules/io/reads_io => common/io/reads}/filtering_reader_wrapper.hpp (100%)
create mode 100644 src/common/io/reads/io_helper.hpp
create mode 100644 src/common/io/reads/ireader.hpp
create mode 100644 src/common/io/reads/ireadstream.hpp
create mode 100644 src/common/io/reads/modifying_reader_wrapper.hpp
rename src/{modules/io/reads_io => common/io/reads}/mpmc_bounded.hpp (100%)
rename src/{modules/io/reads_io => common/io/reads}/multifile_reader.hpp (100%)
rename src/{modules/io/reads_io => common/io/reads}/orientation.hpp (100%)
create mode 100644 src/common/io/reads/osequencestream.hpp
rename src/{modules => common}/io/reads/paired_read.hpp (100%)
create mode 100644 src/common/io/reads/paired_readers.hpp
create mode 100644 src/common/io/reads/parser.cpp
create mode 100644 src/common/io/reads/parser.hpp
rename src/{modules/io/reads_io => common/io/reads}/rc_reader_wrapper.hpp (100%)
create mode 100644 src/common/io/reads/read.hpp
create mode 100644 src/common/io/reads/read_processor.hpp
create mode 100644 src/common/io/reads/read_stream_vector.hpp
create mode 100644 src/common/io/reads/sequence_reader.hpp
create mode 100644 src/common/io/reads/single_read.hpp
create mode 100644 src/common/io/reads/splitting_wrapper.hpp
create mode 100644 src/common/io/reads/vector_reader.hpp
create mode 100644 src/common/io/reads/wrapper_collection.hpp
create mode 100644 src/common/io/sam/bam_parser.hpp
create mode 100644 src/common/io/sam/bam_reader.hpp
create mode 100644 src/common/io/sam/read.cpp
rename src/{modules/io/sam_io => common/io/sam}/read.hpp (100%)
create mode 100644 src/common/io/sam/sam_reader.cpp
create mode 100644 src/common/io/sam/sam_reader.hpp
create mode 100644 src/common/math/smooth.hpp
rename src/{modules => common}/math/xmath.h (100%)
create mode 100644 src/common/modules/CMakeLists.txt
create mode 100644 src/common/modules/alignment/bwa_index.cpp
create mode 100644 src/common/modules/alignment/bwa_index.hpp
create mode 100644 src/common/modules/alignment/bwa_sequence_mapper.hpp
create mode 100644 src/common/modules/alignment/edge_index.hpp
create mode 100644 src/common/modules/alignment/edge_index_refiller.cpp
rename src/{modules/assembly_graph/graph_alignment => common/modules/alignment}/edge_index_refiller.hpp (100%)
create mode 100644 src/common/modules/alignment/kmer_map.hpp
create mode 100644 src/common/modules/alignment/kmer_mapper.hpp
create mode 100644 src/common/modules/alignment/kmer_mapper_logger.hpp
create mode 100644 src/common/modules/alignment/long_read_mapper.hpp
create mode 100644 src/common/modules/alignment/long_read_storage.hpp
create mode 100644 src/common/modules/alignment/pacbio/pac_index.hpp
create mode 100644 src/common/modules/alignment/pacbio/pacbio_read_structures.hpp
create mode 100644 src/common/modules/alignment/sequence_mapper.hpp
create mode 100644 src/common/modules/alignment/sequence_mapper_notifier.hpp
create mode 100644 src/common/modules/alignment/short_read_mapper.hpp
create mode 100644 src/common/modules/genome_consistance_checker.cpp
create mode 100644 src/common/modules/genome_consistance_checker.hpp
create mode 100644 src/common/modules/graph_construction.hpp
create mode 100644 src/common/modules/graph_read_correction.hpp
create mode 100644 src/common/modules/mismatch_shall_not_pass.hpp
create mode 100644 src/common/modules/path_extend/CMakeLists.txt
create mode 100644 src/common/modules/path_extend/extension_chooser.hpp
rename src/{modules/algorithms => common/modules}/path_extend/ideal_pair_info.hpp (100%)
create mode 100644 src/common/modules/path_extend/loop_traverser.hpp
create mode 100644 src/common/modules/path_extend/overlap_analysis.hpp
create mode 100644 src/common/modules/path_extend/paired_library.hpp
create mode 100644 src/common/modules/path_extend/path_extender.hpp
create mode 100644 src/common/modules/path_extend/path_filter.hpp
create mode 100644 src/common/modules/path_extend/path_visualizer.hpp
create mode 100644 src/common/modules/path_extend/pe_config_struct.cpp
create mode 100644 src/common/modules/path_extend/pe_config_struct.hpp
create mode 100644 src/common/modules/path_extend/pe_resolver.hpp
create mode 100644 src/common/modules/path_extend/pe_utils.hpp
create mode 100644 src/common/modules/path_extend/pipeline/extenders_logic.cpp
create mode 100644 src/common/modules/path_extend/pipeline/extenders_logic.hpp
create mode 100644 src/common/modules/path_extend/pipeline/launch_support.cpp
create mode 100644 src/common/modules/path_extend/pipeline/launch_support.hpp
create mode 100644 src/common/modules/path_extend/pipeline/launcher.cpp
create mode 100644 src/common/modules/path_extend/pipeline/launcher.hpp
create mode 100644 src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp
create mode 100644 src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp
create mode 100644 src/common/modules/path_extend/scaffolder2015/extension_chooser2015.cpp
create mode 100644 src/common/modules/path_extend/scaffolder2015/extension_chooser2015.hpp
create mode 100644 src/common/modules/path_extend/scaffolder2015/path_polisher.cpp
create mode 100644 src/common/modules/path_extend/scaffolder2015/path_polisher.hpp
create mode 100644 src/common/modules/path_extend/scaffolder2015/scaffold_graph.cpp
create mode 100644 src/common/modules/path_extend/scaffolder2015/scaffold_graph.hpp
create mode 100644 src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.cpp
create mode 100644 src/common/modules/path_extend/scaffolder2015/scaffold_graph_constructor.hpp
create mode 100644 src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp
create mode 100644 src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp
create mode 100644 src/common/modules/path_extend/split_graph_pair_info.hpp
create mode 100644 src/common/modules/path_extend/weight_counter.hpp
create mode 100644 src/common/modules/simplification/bulge_remover.hpp
create mode 100644 src/common/modules/simplification/cleaner.hpp
create mode 100644 src/common/modules/simplification/complex_bulge_remover.hpp
create mode 100644 src/common/modules/simplification/complex_tip_clipper.hpp
create mode 100644 src/common/modules/simplification/compressor.hpp
create mode 100644 src/common/modules/simplification/dominated_set_finder.hpp
create mode 100644 src/common/modules/simplification/ec_threshold_finder.hpp
create mode 100644 src/common/modules/simplification/erroneous_connection_remover.hpp
rename src/{modules/algorithms => common/modules}/simplification/mf_ec_remover.hpp (100%)
create mode 100644 src/common/modules/simplification/parallel_simplification_algorithms.hpp
create mode 100644 src/common/modules/simplification/relative_coverage_remover.hpp
create mode 100644 src/common/modules/simplification/tip_clipper.hpp
create mode 100644 src/common/modules/simplification/topological_edge_conditions.hpp
create mode 100644 src/common/paired_info/concurrent_pair_info_buffer.hpp
create mode 100644 src/common/paired_info/data_divider.hpp
create mode 100644 src/common/paired_info/distance_estimation.hpp
create mode 100644 src/common/paired_info/histogram.hpp
create mode 100644 src/common/paired_info/histptr.hpp
rename src/{modules => common}/paired_info/index_point.hpp (100%)
create mode 100644 src/common/paired_info/insert_size_refiner.hpp
create mode 100644 src/common/paired_info/is_counter.hpp
create mode 100644 src/common/paired_info/pair_info_bounds.hpp
create mode 100644 src/common/paired_info/pair_info_filler.hpp
rename src/{modules => common}/paired_info/pair_info_filters.hpp (100%)
create mode 100644 src/common/paired_info/pair_info_improver.hpp
create mode 100644 src/common/paired_info/paired_info.hpp
create mode 100644 src/common/paired_info/paired_info_buffer.hpp
rename src/{modules => common}/paired_info/paired_info_helpers.hpp (100%)
create mode 100644 src/common/paired_info/peak_finder.hpp
create mode 100644 src/common/paired_info/smoothing_distance_estimation.hpp
create mode 100644 src/common/paired_info/split_path_constructor.hpp
create mode 100644 src/common/paired_info/weighted_distance_estimation.hpp
create mode 100644 src/common/paired_info/weights.hpp
rename src/{modules => common}/pipeline/CMakeLists.txt (100%)
create mode 100755 src/common/pipeline/config_common.hpp
create mode 100644 src/common/pipeline/config_singl.hpp
create mode 100644 src/common/pipeline/config_struct.cpp
create mode 100644 src/common/pipeline/config_struct.hpp
rename src/{modules => common}/pipeline/genomic_info.hpp (100%)
create mode 100644 src/common/pipeline/genomic_info_filler.cpp
rename src/{modules => common}/pipeline/genomic_info_filler.hpp (100%)
create mode 100644 src/common/pipeline/graph_pack.hpp
create mode 100644 src/common/pipeline/graphio.hpp
create mode 100644 src/common/pipeline/library.cpp
create mode 100644 src/common/pipeline/library.hpp
rename src/{modules => common}/pipeline/library.inl (100%)
create mode 100644 src/common/pipeline/stage.cpp
rename src/{modules => common}/pipeline/stage.hpp (100%)
create mode 100644 src/common/sequence/genome_storage.hpp
create mode 100755 src/common/sequence/nucl.hpp
rename src/{modules/data_structures => common}/sequence/quality.hpp (100%)
create mode 100644 src/common/sequence/rtseq.hpp
create mode 100755 src/common/sequence/seq.hpp
create mode 100644 src/common/sequence/seq_common.hpp
create mode 100755 src/common/sequence/sequence.hpp
create mode 100644 src/common/sequence/sequence_tools.hpp
create mode 100644 src/common/sequence/simple_seq.hpp
rename src/{modules => common}/stages/CMakeLists.txt (100%)
create mode 100644 src/common/stages/construction.cpp
rename src/{modules => common}/stages/construction.hpp (100%)
create mode 100644 src/common/stages/simplification.cpp
rename src/{modules => common}/stages/simplification.hpp (100%)
create mode 100644 src/common/stages/simplification_pipeline/graph_simplification.hpp
create mode 100644 src/common/stages/simplification_pipeline/rna_simplification.hpp
create mode 100644 src/common/stages/simplification_pipeline/simplification_settings.hpp
create mode 100644 src/common/stages/simplification_pipeline/single_cell_simplification.hpp
create mode 100644 src/common/utils/CMakeLists.txt
create mode 100644 src/common/utils/autocompletion.cpp
rename src/{modules/dev_support => common/utils}/autocompletion.hpp (100%)
create mode 100644 src/common/utils/copy_file.cpp
create mode 100644 src/common/utils/copy_file.hpp
create mode 100644 src/common/utils/coverage_model/CMakeLists.txt
create mode 100644 src/common/utils/coverage_model/kmer_coverage_model.cpp
create mode 100644 src/common/utils/coverage_model/kmer_coverage_model.hpp
rename src/{modules/dev_support => common/utils}/cpp_utils.hpp (100%)
create mode 100644 src/common/utils/debruijn_graph/debruijn_graph_constructor.hpp
create mode 100644 src/common/utils/debruijn_graph/early_simplification.hpp
create mode 100644 src/common/utils/file_limit.hpp
create mode 100644 src/common/utils/indices/edge_index_builders.hpp
create mode 100644 src/common/utils/indices/edge_info_updater.hpp
create mode 100644 src/common/utils/indices/edge_multi_index.hpp
create mode 100644 src/common/utils/indices/edge_position_index.hpp
create mode 100644 src/common/utils/indices/editable_index.hpp
create mode 100644 src/common/utils/indices/key_with_hash.hpp
create mode 100644 src/common/utils/indices/kmer_extension_index.hpp
create mode 100644 src/common/utils/indices/kmer_extension_index_builder.hpp
create mode 100644 src/common/utils/indices/kmer_splitters.hpp
create mode 100644 src/common/utils/indices/perfect_hash_map.hpp
create mode 100644 src/common/utils/indices/perfect_hash_map_builder.hpp
create mode 100644 src/common/utils/indices/storing_traits.hpp
rename src/{modules/data_structures => common/utils}/indices/values.hpp (100%)
create mode 100644 src/common/utils/levenshtein.hpp
rename src/{modules/dev_support => common/utils}/log.hpp (100%)
create mode 100644 src/common/utils/logger/log_writers.hpp
create mode 100644 src/common/utils/logger/logger.hpp
create mode 100644 src/common/utils/logger/logger_impl.cpp
rename src/{modules/dev_support => common/utils}/md5.h (100%)
rename src/{modules/dev_support => common/utils}/memory.hpp (100%)
rename src/{modules/dev_support => common/utils}/memory_limit.hpp (100%)
rename src/{modules/data_structures => common/utils}/mph_index/CMakeLists.txt (100%)
rename src/{modules/data_structures => common/utils}/mph_index/base_hash.hpp (100%)
rename src/{modules/data_structures => common/utils}/mph_index/bitpair_vector.cpp (100%)
rename src/{modules/data_structures => common/utils}/mph_index/bitpair_vector.hpp (100%)
rename src/{modules/data_structures => common/utils}/mph_index/common.hpp (100%)
rename src/{modules/data_structures => common/utils}/mph_index/emphf_config.hpp (100%)
rename src/{modules/data_structures => common/utils}/mph_index/hypergraph.hpp (100%)
create mode 100644 src/common/utils/mph_index/hypergraph_sorter_seq.hpp
rename src/{modules/data_structures => common/utils}/mph_index/kmer_index.hpp (100%)
create mode 100644 src/common/utils/mph_index/kmer_index_builder.hpp
create mode 100644 src/common/utils/mph_index/kmer_index_traits.hpp
create mode 100644 src/common/utils/mph_index/mphf.hpp
rename src/{modules/data_structures => common/utils}/mph_index/ranked_bitpair_vector.hpp (100%)
rename src/{modules/dev_support => common/utils}/openmp_wrapper.h (100%)
rename src/{modules/dev_support => common/utils}/parallel_wrapper.hpp (100%)
create mode 100644 src/common/utils/path_helper.cpp
create mode 100644 src/common/utils/path_helper.hpp
rename src/{modules/dev_support => common/utils}/perfcounter.hpp (100%)
create mode 100644 src/common/utils/range.hpp
create mode 100644 src/common/utils/segfault_handler.hpp
create mode 100644 src/common/utils/simple_tools.hpp
rename src/{modules/dev_support => common/utils}/stacktrace.hpp (100%)
create mode 100644 src/common/utils/standard_base.hpp
create mode 100644 src/common/utils/verify.hpp
create mode 100644 src/common/visualization/graph_colorer.hpp
create mode 100644 src/common/visualization/graph_labeler.hpp
create mode 100755 src/common/visualization/graph_print_utils.hpp
create mode 100644 src/common/visualization/graph_printer.hpp
create mode 100644 src/common/visualization/position_filler.hpp
create mode 100644 src/common/visualization/printing_parameter_storage.hpp
create mode 100644 src/common/visualization/vertex_linker.hpp
rename src/{modules => common}/visualization/visualization.hpp (100%)
create mode 100644 src/common/visualization/visualization_utils.hpp
create mode 100644 src/common/visualization/visualizers.hpp
delete mode 100644 src/modules/CMakeLists.txt
delete mode 100644 src/modules/algorithms/CMakeLists.txt
delete mode 100644 src/modules/algorithms/dijkstra/dijkstra_algorithm.hpp
delete mode 100644 src/modules/algorithms/dijkstra/dijkstra_helper.hpp
delete mode 100644 src/modules/algorithms/dijkstra/length_calculator.hpp
delete mode 100644 src/modules/algorithms/genome_consistance_checker.cpp
delete mode 100644 src/modules/algorithms/genome_consistance_checker.hpp
delete mode 100644 src/modules/algorithms/graph_construction.hpp
delete mode 100644 src/modules/algorithms/graph_read_correction.hpp
delete mode 100644 src/modules/algorithms/mismatch_shall_not_pass.hpp
delete mode 100644 src/modules/algorithms/path_extend/CMakeLists.txt
delete mode 100644 src/modules/algorithms/path_extend/extension_chooser.hpp
delete mode 100644 src/modules/algorithms/path_extend/loop_traverser.hpp
delete mode 100644 src/modules/algorithms/path_extend/next_path_searcher.hpp
delete mode 100644 src/modules/algorithms/path_extend/overlap_analysis.hpp
delete mode 100644 src/modules/algorithms/path_extend/paired_library.hpp
delete mode 100644 src/modules/algorithms/path_extend/path_extend_launch.hpp
delete mode 100644 src/modules/algorithms/path_extend/path_extender.hpp
delete mode 100644 src/modules/algorithms/path_extend/path_filter.hpp
delete mode 100644 src/modules/algorithms/path_extend/path_visualizer.hpp
delete mode 100644 src/modules/algorithms/path_extend/pe_config_struct.cpp
delete mode 100644 src/modules/algorithms/path_extend/pe_config_struct.hpp
delete mode 100644 src/modules/algorithms/path_extend/pe_io.hpp
delete mode 100644 src/modules/algorithms/path_extend/pe_resolver.hpp
delete mode 100644 src/modules/algorithms/path_extend/pe_utils.hpp
delete mode 100644 src/modules/algorithms/path_extend/scaffolder2015/connection_condition2015.cpp
delete mode 100644 src/modules/algorithms/path_extend/scaffolder2015/connection_condition2015.hpp
delete mode 100644 src/modules/algorithms/path_extend/scaffolder2015/extension_chooser2015.cpp
delete mode 100644 src/modules/algorithms/path_extend/scaffolder2015/extension_chooser2015.hpp
delete mode 100644 src/modules/algorithms/path_extend/scaffolder2015/scaffold_graph.cpp
delete mode 100644 src/modules/algorithms/path_extend/scaffolder2015/scaffold_graph.hpp
delete mode 100644 src/modules/algorithms/path_extend/scaffolder2015/scaffold_graph_constructor.cpp
delete mode 100644 src/modules/algorithms/path_extend/scaffolder2015/scaffold_graph_constructor.hpp
delete mode 100644 src/modules/algorithms/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp
delete mode 100644 src/modules/algorithms/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp
delete mode 100644 src/modules/algorithms/path_extend/split_graph_pair_info.hpp
delete mode 100644 src/modules/algorithms/path_extend/weight_counter.hpp
delete mode 100644 src/modules/algorithms/simplification/bulge_remover.hpp
delete mode 100644 src/modules/algorithms/simplification/cleaner.hpp
delete mode 100644 src/modules/algorithms/simplification/complex_bulge_remover.hpp
delete mode 100644 src/modules/algorithms/simplification/complex_tip_clipper.hpp
delete mode 100644 src/modules/algorithms/simplification/compressor.hpp
delete mode 100644 src/modules/algorithms/simplification/dominated_set_finder.hpp
delete mode 100644 src/modules/algorithms/simplification/ec_threshold_finder.hpp
delete mode 100644 src/modules/algorithms/simplification/erroneous_connection_remover.hpp
delete mode 100644 src/modules/algorithms/simplification/parallel_simplification_algorithms.hpp
delete mode 100644 src/modules/algorithms/simplification/relative_coverage_remover.hpp
delete mode 100644 src/modules/algorithms/simplification/tip_clipper.hpp
delete mode 100644 src/modules/assembly_graph/CMakeLists.txt
delete mode 100644 src/modules/assembly_graph/components/connected_component.hpp
delete mode 100644 src/modules/assembly_graph/components/graph_component.hpp
delete mode 100644 src/modules/assembly_graph/components/splitters.hpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/edge_index.hpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/edge_index_refiller.cpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/kmer_map.hpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/kmer_mapper.hpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/kmer_mapper_logger.hpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/long_read_mapper.hpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/long_read_storage.hpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/pacbio/pac_index.hpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/pacbio/pacbio_gap_closer.hpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/pacbio/pacbio_read_structures.hpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/sequence_mapper.hpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/sequence_mapper_notifier.hpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/short_read_mapper.hpp
delete mode 100644 src/modules/assembly_graph/graph_core/action_handlers.hpp
delete mode 100644 src/modules/assembly_graph/graph_core/basic_graph_stats.hpp
delete mode 100644 src/modules/assembly_graph/graph_core/construction_helper.hpp
delete mode 100644 src/modules/assembly_graph/graph_core/coverage.hpp
delete mode 100644 src/modules/assembly_graph/graph_core/debruijn_data.hpp
delete mode 100644 src/modules/assembly_graph/graph_core/graph_core.hpp
delete mode 100644 src/modules/assembly_graph/graph_core/graph_iterators.hpp
delete mode 100644 src/modules/assembly_graph/graph_core/observable_graph.hpp
delete mode 100644 src/modules/assembly_graph/graph_core/order_and_law.hpp
delete mode 100644 src/modules/assembly_graph/graph_support/basic_edge_conditions.hpp
delete mode 100644 src/modules/assembly_graph/graph_support/basic_vertex_conditions.hpp
delete mode 100644 src/modules/assembly_graph/graph_support/contig_output.hpp
delete mode 100644 src/modules/assembly_graph/graph_support/detail_coverage.hpp
delete mode 100644 src/modules/assembly_graph/graph_support/genomic_quality.hpp
delete mode 100644 src/modules/assembly_graph/graph_support/graph_processing_algorithm.hpp
delete mode 100644 src/modules/assembly_graph/graph_support/parallel_processing.hpp
delete mode 100644 src/modules/assembly_graph/graph_support/scaff_supplementary.cpp
delete mode 100644 src/modules/assembly_graph/graph_support/scaff_supplementary.hpp
delete mode 100644 src/modules/assembly_graph/handlers/edge_labels_handler.hpp
delete mode 100644 src/modules/assembly_graph/handlers/edges_position_handler.hpp
delete mode 100644 src/modules/assembly_graph/handlers/id_track_handler.hpp
delete mode 100644 src/modules/assembly_graph/paths/bidirectional_path.cpp
delete mode 100644 src/modules/assembly_graph/paths/bidirectional_path.hpp
delete mode 100644 src/modules/assembly_graph/paths/mapping_path.hpp
delete mode 100644 src/modules/assembly_graph/paths/path_finders.hpp
delete mode 100644 src/modules/assembly_graph/paths/path_processor.hpp
delete mode 100644 src/modules/assembly_graph/paths/path_utils.hpp
delete mode 100644 src/modules/assembly_graph/stats/picture_dump.hpp
delete mode 100644 src/modules/assembly_graph/stats/statistics.hpp
delete mode 100644 src/modules/data_structures/debruijn_graph/debruijn_graph_constructor.hpp
delete mode 100644 src/modules/data_structures/debruijn_graph/early_simplification.hpp
delete mode 100644 src/modules/data_structures/indices/edge_index_builders.hpp
delete mode 100644 src/modules/data_structures/indices/edge_info_updater.hpp
delete mode 100644 src/modules/data_structures/indices/edge_multi_index.hpp
delete mode 100644 src/modules/data_structures/indices/edge_position_index.hpp
delete mode 100644 src/modules/data_structures/indices/editable_index.hpp
delete mode 100644 src/modules/data_structures/indices/key_with_hash.hpp
delete mode 100644 src/modules/data_structures/indices/kmer_extension_index.hpp
delete mode 100644 src/modules/data_structures/indices/kmer_extension_index_builder.hpp
delete mode 100644 src/modules/data_structures/indices/kmer_splitters.hpp
delete mode 100644 src/modules/data_structures/indices/perfect_hash_map.hpp
delete mode 100644 src/modules/data_structures/indices/perfect_hash_map_builder.hpp
delete mode 100644 src/modules/data_structures/indices/storing_traits.hpp
delete mode 100644 src/modules/data_structures/mph_index/hypergraph_sorter_seq.hpp
delete mode 100644 src/modules/data_structures/mph_index/kmer_index_builder.hpp
delete mode 100644 src/modules/data_structures/mph_index/kmer_index_traits.hpp
delete mode 100644 src/modules/data_structures/mph_index/mphf.hpp
delete mode 100644 src/modules/data_structures/sequence/CMakeLists.txt
delete mode 100644 src/modules/data_structures/sequence/genome_storage.cpp
delete mode 100644 src/modules/data_structures/sequence/genome_storage.hpp
delete mode 100755 src/modules/data_structures/sequence/nucl.hpp
delete mode 100644 src/modules/data_structures/sequence/rtseq.hpp
delete mode 100644 src/modules/data_structures/sequence/runtime_k.hpp
delete mode 100755 src/modules/data_structures/sequence/seq.hpp
delete mode 100644 src/modules/data_structures/sequence/seq_common.hpp
delete mode 100755 src/modules/data_structures/sequence/sequence.hpp
delete mode 100644 src/modules/data_structures/sequence/sequence_tools.hpp
delete mode 100644 src/modules/data_structures/sequence/simple_seq.hpp
delete mode 100644 src/modules/dev_support/CMakeLists.txt
delete mode 100644 src/modules/dev_support/autocompletion.cpp
delete mode 100644 src/modules/dev_support/copy_file.cpp
delete mode 100644 src/modules/dev_support/copy_file.hpp
delete mode 100644 src/modules/dev_support/file_limit.hpp
delete mode 100644 src/modules/dev_support/func.hpp
delete mode 100644 src/modules/dev_support/logger/log_writers.hpp
delete mode 100644 src/modules/dev_support/logger/logger.hpp
delete mode 100644 src/modules/dev_support/logger/logger_impl.cpp
delete mode 100644 src/modules/dev_support/path_helper.cpp
delete mode 100644 src/modules/dev_support/path_helper.hpp
delete mode 100644 src/modules/dev_support/range.hpp
delete mode 100644 src/modules/dev_support/segfault_handler.hpp
delete mode 100644 src/modules/dev_support/simple_tools.hpp
delete mode 100644 src/modules/dev_support/standard_base.hpp
delete mode 100644 src/modules/dev_support/verify.hpp
delete mode 100644 src/modules/io/CMakeLists.txt
delete mode 100644 src/modules/io/dataset_support/dataset_readers.hpp
delete mode 100644 src/modules/io/dataset_support/read_converter.hpp
delete mode 100755 src/modules/io/graph_io/graph_print_utils.hpp
delete mode 100644 src/modules/io/kmers_io/kmer_iterator.hpp
delete mode 100644 src/modules/io/kmers_io/mmapped_reader.hpp
delete mode 100644 src/modules/io/kmers_io/mmapped_writer.hpp
delete mode 100644 src/modules/io/reads/read.hpp
delete mode 100644 src/modules/io/reads/single_read.hpp
delete mode 100644 src/modules/io/reads_io/binary_converter.hpp
delete mode 100644 src/modules/io/reads_io/binary_streams.hpp
delete mode 100644 src/modules/io/reads_io/careful_filtering_reader_wrapper.hpp
delete mode 100644 src/modules/io/reads_io/cutting_reader_wrapper.hpp
delete mode 100644 src/modules/io/reads_io/easy_reader.hpp
delete mode 100644 src/modules/io/reads_io/fasta_fastq_gz_parser.hpp
delete mode 100644 src/modules/io/reads_io/file_reader.hpp
delete mode 100644 src/modules/io/reads_io/io_helper.hpp
delete mode 100644 src/modules/io/reads_io/ireader.hpp
delete mode 100644 src/modules/io/reads_io/ireadstream.hpp
delete mode 100644 src/modules/io/reads_io/is_corrupting_wrapper.hpp
delete mode 100644 src/modules/io/reads_io/modifying_reader_wrapper.hpp
delete mode 100644 src/modules/io/reads_io/osequencestream.hpp
delete mode 100644 src/modules/io/reads_io/paired_readers.hpp
delete mode 100644 src/modules/io/reads_io/parser.cpp
delete mode 100644 src/modules/io/reads_io/parser.hpp
delete mode 100644 src/modules/io/reads_io/read_processor.hpp
delete mode 100644 src/modules/io/reads_io/read_stream_vector.hpp
delete mode 100644 src/modules/io/reads_io/sequence_reader.hpp
delete mode 100644 src/modules/io/reads_io/splitting_wrapper.hpp
delete mode 100644 src/modules/io/reads_io/vector_reader.hpp
delete mode 100644 src/modules/io/reads_io/wrapper_collection.hpp
delete mode 100644 src/modules/io/sam_io/bam_parser.hpp
delete mode 100644 src/modules/io/sam_io/bam_reader.hpp
delete mode 100644 src/modules/io/sam_io/read.cpp
delete mode 100644 src/modules/io/sam_io/sam_reader.cpp
delete mode 100644 src/modules/io/sam_io/sam_reader.hpp
delete mode 100644 src/modules/math/CMakeLists.txt
delete mode 100644 src/modules/math/kmer_coverage_model.cpp
delete mode 100644 src/modules/math/kmer_coverage_model.hpp
delete mode 100644 src/modules/math/pred.hpp
delete mode 100644 src/modules/math/smooth.hpp
delete mode 100644 src/modules/paired_info/CMakeLists.txt
delete mode 100644 src/modules/paired_info/bwa_pair_info_filler.cpp
delete mode 100644 src/modules/paired_info/bwa_pair_info_filler.hpp
delete mode 100644 src/modules/paired_info/data_divider.hpp
delete mode 100644 src/modules/paired_info/distance_estimation.hpp
delete mode 100644 src/modules/paired_info/histogram.hpp
delete mode 100644 src/modules/paired_info/insert_size_refiner.hpp
delete mode 100644 src/modules/paired_info/is_counter.hpp
delete mode 100644 src/modules/paired_info/pair_info_bounds.hpp
delete mode 100644 src/modules/paired_info/pair_info_filler.hpp
delete mode 100644 src/modules/paired_info/pair_info_improver.hpp
delete mode 100644 src/modules/paired_info/paired_info.hpp
delete mode 100644 src/modules/paired_info/peak_finder.hpp
delete mode 100644 src/modules/paired_info/smoothing_distance_estimation.hpp
delete mode 100644 src/modules/paired_info/split_path_constructor.hpp
delete mode 100644 src/modules/paired_info/weighted_distance_estimation.hpp
delete mode 100644 src/modules/paired_info/weights.hpp
delete mode 100755 src/modules/pipeline/config_common.hpp
delete mode 100644 src/modules/pipeline/config_singl.hpp
delete mode 100644 src/modules/pipeline/config_struct.cpp
delete mode 100644 src/modules/pipeline/config_struct.hpp
delete mode 100644 src/modules/pipeline/genomic_info_filler.cpp
delete mode 100644 src/modules/pipeline/graph_pack.hpp
delete mode 100644 src/modules/pipeline/graphio.hpp
delete mode 100644 src/modules/pipeline/library.cpp
delete mode 100644 src/modules/pipeline/library.hpp
delete mode 100644 src/modules/pipeline/stage.cpp
delete mode 100644 src/modules/stages/construction.cpp
delete mode 100644 src/modules/stages/simplification.cpp
delete mode 100644 src/modules/stages/simplification_pipeline/graph_simplification.hpp
delete mode 100644 src/modules/stages/simplification_pipeline/simplification_settings.hpp
delete mode 100644 src/modules/stages/simplification_pipeline/single_cell_simplification.hpp
delete mode 100644 src/modules/visualization/graph_colorer.hpp
delete mode 100644 src/modules/visualization/graph_labeler.hpp
delete mode 100644 src/modules/visualization/graph_printer.hpp
delete mode 100644 src/modules/visualization/position_filler.hpp
delete mode 100644 src/modules/visualization/printing_parameter_storage.hpp
delete mode 100644 src/modules/visualization/vertex_linker.hpp
delete mode 100644 src/modules/visualization/visualization_utils.hpp
delete mode 100644 src/modules/visualization/visualizers.hpp
create mode 100644 src/projects/cclean/CMakeLists.txt
create mode 100644 src/projects/cclean/adapter_index.cpp
create mode 100644 src/projects/cclean/adapter_index.hpp
create mode 100644 src/projects/cclean/additional.cpp
create mode 100644 src/projects/cclean/brute_force_clean.cpp
create mode 100644 src/projects/cclean/brute_force_clean.hpp
create mode 100644 src/projects/cclean/comparator.hpp
create mode 100644 src/projects/cclean/config_struct_cclean.cpp
create mode 100644 src/projects/cclean/config_struct_cclean.hpp
create mode 100644 src/projects/cclean/job_wrappers.cpp
create mode 100644 src/projects/cclean/job_wrappers.hpp
create mode 100644 src/projects/cclean/main.cpp
create mode 100644 src/projects/cclean/output.cpp
create mode 100644 src/projects/cclean/output.hpp
create mode 100644 src/projects/cclean/running_modes.cpp
create mode 100644 src/projects/cclean/running_modes.hpp
create mode 100644 src/projects/cclean/utils.cpp
create mode 100644 src/projects/cclean/utils.hpp
create mode 100644 src/projects/cclean/valid_kmer_generator.hpp
create mode 100644 src/projects/mts/CMakeLists.txt
create mode 100644 src/projects/mts/Common.snake
create mode 100644 src/projects/mts/README
create mode 100644 src/projects/mts/Snakefile
create mode 100644 src/projects/mts/Stats.snake
create mode 100644 src/projects/mts/annotation.hpp
create mode 100644 src/projects/mts/config.yaml
create mode 100644 src/projects/mts/contig_abundance.cpp
create mode 100644 src/projects/mts/contig_abundance.hpp
create mode 100644 src/projects/mts/contig_abundance_counter.cpp
create mode 100644 src/projects/mts/formats.hpp
create mode 100644 src/projects/mts/kmc_api/kmc_file.cpp
create mode 100644 src/projects/mts/kmc_api/kmc_file.h
create mode 100644 src/projects/mts/kmc_api/kmer_api.cpp
create mode 100644 src/projects/mts/kmc_api/kmer_api.h
create mode 100644 src/projects/mts/kmc_api/kmer_defs.h
create mode 100644 src/projects/mts/kmc_api/mmer.cpp
create mode 100644 src/projects/mts/kmc_api/mmer.h
create mode 100644 src/projects/mts/kmc_api/stdafx.h
create mode 100644 src/projects/mts/kmer_multiplicity_counter.cpp
create mode 100644 src/projects/mts/log.properties
create mode 100644 src/projects/mts/logger.hpp
create mode 100755 src/projects/mts/mts.py
create mode 100644 src/projects/mts/prop_binning.cpp
create mode 100644 src/projects/mts/propagate.cpp
create mode 100644 src/projects/mts/propagate.hpp
create mode 100644 src/projects/mts/read_binning.cpp
create mode 100644 src/projects/mts/read_binning.hpp
copy configs/debruijn/simplification.info.template => src/projects/mts/scripts/__init__.py (100%)
create mode 100755 src/projects/mts/scripts/calc_kmers_mpl.py
create mode 100755 src/projects/mts/scripts/canopy_launch.sh
create mode 100755 src/projects/mts/scripts/choose_samples.py
create mode 100755 src/projects/mts/scripts/combine_contigs.py
create mode 100644 src/projects/mts/scripts/common.py
create mode 100755 src/projects/mts/scripts/filter_nucmer.py
create mode 100755 src/projects/mts/scripts/gather_stats.py
create mode 100755 src/projects/mts/scripts/gen_samples.py
create mode 100755 src/projects/mts/scripts/make_input.py
create mode 100755 src/projects/mts/scripts/make_points_matrix.py
create mode 100755 src/projects/mts/scripts/parse_output.py
create mode 100644 src/projects/mts/scripts/pca.R
create mode 100755 src/projects/mts/scripts/ref_stats.sh
create mode 100755 src/projects/mts/scripts/split_bins.py
create mode 100644 src/projects/mts/stats.cpp
create mode 100755 src/projects/mts/test.py
create mode 100644 src/projects/mts/visualization.hpp
create mode 100644 src/projects/spades/contig_output_stage.cpp
create mode 100644 src/projects/spades/contig_output_stage.hpp
create mode 100644 src/projects/spades/gap_closing.hpp
create mode 100644 src/projects/spades/hybrid_aligning.cpp
create mode 100644 src/projects/spades/hybrid_aligning.hpp
create mode 100644 src/projects/spades/hybrid_gap_closer.hpp
delete mode 100644 src/projects/spades/pacbio_aligning.cpp
delete mode 100644 src/projects/spades/pacbio_aligning.hpp
create mode 100644 src/projects/spades/series_analysis.hpp
delete mode 100644 src/utils/adt/bag.hpp
delete mode 100644 src/utils/adt/concurrent_dsu.hpp
delete mode 100644 src/utils/adt/function_traits.hpp
delete mode 100644 src/utils/adt/kmer_hash_vector.hpp
delete mode 100644 src/utils/adt/kmer_vector.hpp
delete mode 100644 src/utils/adt/parallel_seq_vector.hpp
delete mode 100644 src/utils/adt/queue_iterator.hpp
delete mode 100644 src/utils/levenshtein.hpp
create mode 100644 test_dataset_plasmid/pl1.fq.gz
create mode 100644 test_dataset_plasmid/pl2.fq.gz
--
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git
More information about the debian-med-commit
mailing list