[med-svn] [spades] branch upstream updated (fb140eb -> 34bcf2c)
Michael Crusoe
misterc-guest at moszumanska.debian.org
Wed Apr 19 13:24:40 UTC 2017
This is an automated email from the git hooks/post-receive script.
misterc-guest pushed a change to branch upstream
in repository spades.
from fb140eb New upstream version 3.9.1+dfsg
new 34bcf2c New upstream version 3.10.1+dfsg
The 1 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 +
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 +
.../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 +
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test_dataset_plasmid/pl2.fq.gz | Bin 0 -> 68276 bytes
602 files changed, 25877 insertions(+), 13974 deletions(-)
create mode 100644 configs/debruijn/large_genome_mode.info
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create mode 100644 ext/include/bwa/utils.h
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create mode 100644 src/common/modules/path_extend/scaffolder2015/connection_condition2015.cpp
create mode 100644 src/common/modules/path_extend/scaffolder2015/connection_condition2015.hpp
rename src/{modules/algorithms => common/modules}/path_extend/scaffolder2015/extension_chooser2015.cpp (71%)
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
rename src/{modules/algorithms => common/modules}/path_extend/scaffolder2015/scaffold_graph.cpp (89%)
rename src/{modules/algorithms => common/modules}/path_extend/scaffolder2015/scaffold_graph.hpp (91%)
rename src/{modules/algorithms => common/modules}/path_extend/scaffolder2015/scaffold_graph_constructor.cpp (87%)
rename src/{modules/algorithms => common/modules}/path_extend/scaffolder2015/scaffold_graph_constructor.hpp (78%)
rename src/{modules/algorithms => common/modules}/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp (69%)
create mode 100644 src/common/modules/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp
rename src/{modules/algorithms => common/modules}/path_extend/split_graph_pair_info.hpp (96%)
create mode 100644 src/common/modules/path_extend/weight_counter.hpp
rename src/{modules/algorithms => common/modules}/simplification/bulge_remover.hpp (79%)
rename src/{modules/algorithms => common/modules}/simplification/cleaner.hpp (64%)
rename src/{modules/algorithms => common/modules}/simplification/complex_bulge_remover.hpp (80%)
create mode 100644 src/common/modules/simplification/complex_tip_clipper.hpp
rename src/{modules/algorithms => common/modules}/simplification/compressor.hpp (64%)
rename src/{modules/algorithms => common/modules}/simplification/dominated_set_finder.hpp (97%)
rename src/{modules/algorithms => common/modules}/simplification/ec_threshold_finder.hpp (97%)
rename src/{modules/algorithms => common/modules}/simplification/erroneous_connection_remover.hpp (50%)
rename src/{modules/algorithms => common/modules}/simplification/mf_ec_remover.hpp (100%)
rename src/{modules/algorithms => common/modules}/simplification/parallel_simplification_algorithms.hpp (84%)
rename src/{modules/algorithms => common/modules}/simplification/relative_coverage_remover.hpp (69%)
rename src/{modules/algorithms => common/modules}/simplification/tip_clipper.hpp (84%)
rename src/{modules/assembly_graph/graph_support/basic_edge_conditions.hpp => common/modules/simplification/topological_edge_conditions.hpp} (50%)
create mode 100644 src/common/paired_info/concurrent_pair_info_buffer.hpp
rename src/{modules => common}/paired_info/data_divider.hpp (99%)
rename src/{modules => common}/paired_info/distance_estimation.hpp (87%)
rename src/{modules => common}/paired_info/histogram.hpp (93%)
create mode 100644 src/common/paired_info/histptr.hpp
rename src/{modules => common}/paired_info/index_point.hpp (100%)
rename src/{modules => common}/paired_info/insert_size_refiner.hpp (98%)
rename src/{modules => common}/paired_info/is_counter.hpp (68%)
rename src/{modules => common}/paired_info/pair_info_bounds.hpp (96%)
create mode 100644 src/common/paired_info/pair_info_filler.hpp
rename src/{modules => common}/paired_info/pair_info_filters.hpp (100%)
rename src/{modules => common}/paired_info/pair_info_improver.hpp (97%)
rename src/{modules => common}/paired_info/paired_info.hpp (63%)
create mode 100644 src/common/paired_info/paired_info_buffer.hpp
rename src/{modules => common}/paired_info/paired_info_helpers.hpp (100%)
rename src/{modules => common}/paired_info/peak_finder.hpp (99%)
rename src/{modules => common}/paired_info/smoothing_distance_estimation.hpp (98%)
rename src/{modules => common}/paired_info/split_path_constructor.hpp (87%)
rename src/{modules => common}/paired_info/weighted_distance_estimation.hpp (68%)
rename src/{modules => common}/paired_info/weights.hpp (86%)
rename src/{modules => common}/pipeline/CMakeLists.txt (100%)
rename src/{modules => common}/pipeline/config_common.hpp (97%)
rename src/{modules => common}/pipeline/config_singl.hpp (97%)
rename src/{modules => common}/pipeline/config_struct.cpp (92%)
rename src/{modules => common}/pipeline/config_struct.hpp (96%)
rename src/{modules => common}/pipeline/genomic_info.hpp (100%)
rename src/{modules => common}/pipeline/genomic_info_filler.cpp (94%)
rename src/{modules => common}/pipeline/genomic_info_filler.hpp (100%)
rename src/{modules => common}/pipeline/graph_pack.hpp (84%)
rename src/{modules => common}/pipeline/graphio.hpp (97%)
rename src/{modules => common}/pipeline/library.cpp (97%)
rename src/{modules => common}/pipeline/library.hpp (86%)
rename src/{modules => common}/pipeline/library.inl (100%)
rename src/{modules => common}/pipeline/stage.cpp (98%)
rename src/{modules => common}/pipeline/stage.hpp (100%)
rename src/{modules/data_structures/sequence/genome_storage.cpp => common/sequence/genome_storage.hpp} (64%)
rename src/{modules/data_structures => common}/sequence/nucl.hpp (98%)
rename src/{modules/data_structures => common}/sequence/quality.hpp (100%)
rename src/{modules/data_structures => common}/sequence/rtseq.hpp (97%)
rename src/{modules/data_structures => common}/sequence/seq.hpp (99%)
rename src/{modules/data_structures/sequence/runtime_k.hpp => common/sequence/seq_common.hpp} (55%)
rename src/{modules/data_structures => common}/sequence/sequence.hpp (99%)
rename src/{modules/data_structures => common}/sequence/sequence_tools.hpp (97%)
rename src/{modules/data_structures => common}/sequence/simple_seq.hpp (97%)
rename src/{modules => common}/stages/CMakeLists.txt (100%)
rename src/{modules => common}/stages/construction.cpp (90%)
rename src/{modules => common}/stages/construction.hpp (100%)
rename src/{modules => common}/stages/simplification.cpp (71%)
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
rename src/{modules => common}/stages/simplification_pipeline/simplification_settings.hpp (98%)
rename src/{modules => common}/stages/simplification_pipeline/single_cell_simplification.hpp (55%)
rename src/{modules/math => common/utils}/CMakeLists.txt (59%)
rename src/{modules/dev_support => common/utils}/autocompletion.cpp (98%)
rename src/{modules/dev_support => common/utils}/autocompletion.hpp (100%)
rename src/{modules/dev_support => common/utils}/copy_file.cpp (98%)
rename src/{modules/dev_support => common/utils}/copy_file.hpp (94%)
rename src/{modules/paired_info => common/utils/coverage_model}/CMakeLists.txt (70%)
rename src/{modules/math => common/utils/coverage_model}/kmer_coverage_model.cpp (83%)
rename src/{modules/math => common/utils/coverage_model}/kmer_coverage_model.hpp (84%)
rename src/{modules/dev_support => common/utils}/cpp_utils.hpp (100%)
rename src/{modules/data_structures => common/utils}/debruijn_graph/debruijn_graph_constructor.hpp (93%)
rename src/{modules/data_structures => common/utils}/debruijn_graph/early_simplification.hpp (92%)
rename src/{modules/dev_support => common/utils}/file_limit.hpp (96%)
rename src/{modules/data_structures => common/utils}/indices/edge_index_builders.hpp (99%)
rename src/{modules/data_structures => common/utils}/indices/edge_info_updater.hpp (68%)
rename src/{modules/data_structures => common/utils}/indices/edge_multi_index.hpp (98%)
rename src/{modules/data_structures => common/utils}/indices/edge_position_index.hpp (62%)
rename src/{modules/data_structures => common/utils}/indices/editable_index.hpp (94%)
rename src/{modules/data_structures => common/utils}/indices/key_with_hash.hpp (97%)
rename src/{modules/data_structures => common/utils}/indices/kmer_extension_index.hpp (97%)
rename src/{modules/data_structures => common/utils}/indices/kmer_extension_index_builder.hpp (87%)
rename src/{modules/data_structures => common/utils}/indices/kmer_splitters.hpp (94%)
rename src/{modules/data_structures => common/utils}/indices/perfect_hash_map.hpp (86%)
rename src/{modules/data_structures => common/utils}/indices/perfect_hash_map_builder.hpp (93%)
rename src/{modules/data_structures => common/utils}/indices/storing_traits.hpp (56%)
rename src/{modules/data_structures => common/utils}/indices/values.hpp (100%)
rename src/{ => common}/utils/levenshtein.hpp (99%)
rename src/{modules/dev_support => common/utils}/log.hpp (100%)
rename src/{modules/dev_support => common/utils}/logger/log_writers.hpp (97%)
rename src/{modules/dev_support => common/utils}/logger/logger.hpp (99%)
rename src/{modules/dev_support => common/utils}/logger/logger_impl.cpp (98%)
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%)
rename src/{modules/data_structures => common/utils}/mph_index/hypergraph_sorter_seq.hpp (98%)
rename src/{modules/data_structures => common/utils}/mph_index/kmer_index.hpp (100%)
rename src/{modules/data_structures => common/utils}/mph_index/kmer_index_builder.hpp (79%)
rename src/{modules/data_structures => common/utils}/mph_index/kmer_index_traits.hpp (94%)
rename src/{modules/data_structures => common/utils}/mph_index/mphf.hpp (99%)
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%)
rename src/{modules/dev_support => common/utils}/path_helper.cpp (99%)
rename src/{modules/dev_support => common/utils}/path_helper.hpp (96%)
rename src/{modules/dev_support => common/utils}/perfcounter.hpp (100%)
rename src/{modules/dev_support => common/utils}/range.hpp (98%)
rename src/{modules/dev_support => common/utils}/segfault_handler.hpp (97%)
rename src/{modules/dev_support => common/utils}/simple_tools.hpp (94%)
rename src/{modules/dev_support => common/utils}/stacktrace.hpp (100%)
rename src/{modules/dev_support => common/utils}/standard_base.hpp (93%)
rename src/{modules/dev_support => common/utils}/verify.hpp (97%)
rename src/{modules => common}/visualization/graph_colorer.hpp (65%)
rename src/{modules => common}/visualization/graph_labeler.hpp (75%)
rename src/{modules/io/graph_io => common/visualization}/graph_print_utils.hpp (98%)
rename src/{modules => common}/visualization/graph_printer.hpp (51%)
rename src/{modules => common}/visualization/position_filler.hpp (61%)
rename src/{modules => common}/visualization/printing_parameter_storage.hpp (79%)
rename src/{modules => common}/visualization/vertex_linker.hpp (58%)
rename src/{modules => common}/visualization/visualization.hpp (100%)
create mode 100644 src/common/visualization/visualization_utils.hpp
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delete mode 100644 src/modules/CMakeLists.txt
delete mode 100644 src/modules/algorithms/path_extend/next_path_searcher.hpp
delete mode 100644 src/modules/algorithms/path_extend/path_extend_launch.hpp
delete mode 100644 src/modules/algorithms/path_extend/pe_io.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.hpp
delete mode 100644 src/modules/algorithms/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp
delete mode 100644 src/modules/algorithms/path_extend/weight_counter.hpp
delete mode 100644 src/modules/algorithms/simplification/complex_tip_clipper.hpp
delete mode 100644 src/modules/assembly_graph/components/graph_component.hpp
delete mode 100644 src/modules/assembly_graph/graph_alignment/pacbio/pacbio_gap_closer.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/paths/path_utils.hpp
delete mode 100644 src/modules/data_structures/sequence/CMakeLists.txt
delete mode 100644 src/modules/data_structures/sequence/genome_storage.hpp
delete mode 100644 src/modules/dev_support/CMakeLists.txt
delete mode 100644 src/modules/dev_support/func.hpp
delete mode 100644 src/modules/io/dataset_support/dataset_readers.hpp
delete mode 100644 src/modules/io/reads_io/binary_streams.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/is_corrupting_wrapper.hpp
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/pair_info_filler.hpp
delete mode 100644 src/modules/stages/simplification_pipeline/graph_simplification.hpp
delete mode 100644 src/modules/visualization/visualization_utils.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
rename src/{modules/data_structures/sequence/seq_common.hpp => projects/cclean/comparator.hpp} (61%)
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
copy src/projects/{hammer => cclean}/valid_kmer_generator.hpp (85%)
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
rename src/projects/spades/{pacbio_aligning.hpp => hybrid_aligning.hpp} (75%)
create mode 100644 src/projects/spades/hybrid_gap_closer.hpp
delete mode 100644 src/projects/spades/pacbio_aligning.cpp
create mode 100644 src/projects/spades/series_analysis.hpp
create mode 100644 test_dataset_plasmid/pl1.fq.gz
create mode 100644 test_dataset_plasmid/pl2.fq.gz
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