[med-svn] [spades] 01/02: Merge branch 'master' into debian/jessie-backports-sloppy
Andreas Tille
tille at debian.org
Mon Aug 21 07:08:42 UTC 2017
This is an automated email from the git hooks/post-receive script.
tille pushed a commit to tag debian/3.10.1+dfsg-3_bpo8+1
in repository spades.
commit 3a2a5089d0777aa54b01508b8750c4c6b377c3c0
Merge: 117634e fd1116c
Author: Andreas Tille <tille at debian.org>
Date: Mon Aug 21 08:39:36 2017 +0200
Merge branch 'master' into debian/jessie-backports-sloppy
LICENSE | 6 +-
README | 2 +-
VERSION | 2 +-
changelog.html | 33 +-
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 | 31 +
debian/control | 8 +-
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/gcc7.patch | 13 +
debian/patches/series | 3 +
debian/patches/spelling | 118 +
dipspades_manual.html | 4 +-
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 | 119 +-
metaspades.py | 102 +-
plasmidspades.py | 102 +-
rnaspades.py | 102 +-
rnaspades_manual.html | 27 +-
spades.py | 102 +-
spades_compile.sh | 2 +-
src/CMakeLists.txt | 6 +-
src/cmake/options.cmake | 3 +
src/cmake/pack.cmake | 8 +-
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 -
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.../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 | 42 +-
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 | 6 +-
src/projects/mph_test/main.cpp | 27 +-
src/projects/mts/CMakeLists.txt | 57 +
src/projects/mts/Common.snake | 69 +
src/projects/mts/README | 21 +
src/projects/mts/Snakefile | 175 ++
src/projects/mts/Stats.snake | 270 +++
src/projects/mts/annotation.hpp | 310 +++
src/projects/mts/config.yaml | 10 +
src/projects/mts/contig_abundance.cpp | 176 ++
src/projects/mts/contig_abundance.hpp | 143 ++
src/projects/mts/contig_abundance_counter.cpp | 101 +
src/projects/mts/formats.hpp | 29 +
src/projects/mts/kmc_api/kmc_file.cpp | 1093 +++++++++
src/projects/mts/kmc_api/kmc_file.h | 141 ++
src/projects/mts/kmc_api/kmer_api.cpp | 48 +
src/projects/mts/kmc_api/kmer_api.h | 596 +++++
src/projects/mts/kmc_api/kmer_defs.h | 54 +
src/projects/mts/kmc_api/mmer.cpp | 49 +
src/projects/mts/kmc_api/mmer.h | 182 ++
src/projects/mts/kmc_api/stdafx.h | 4 +
src/projects/mts/kmer_multiplicity_counter.cpp | 256 ++
src/projects/mts/log.properties | 10 +
src/projects/mts/logger.hpp | 11 +
src/projects/mts/mts.py | 73 +
src/projects/mts/prop_binning.cpp | 128 +
src/projects/mts/propagate.cpp | 331 +++
src/projects/mts/propagate.hpp | 29 +
src/projects/mts/read_binning.cpp | 90 +
src/projects/mts/read_binning.hpp | 92 +
.../empty.cpp => projects/mts/scripts/__init__.py} | 0
src/projects/mts/scripts/calc_kmers_mpl.py | 38 +
src/projects/mts/scripts/canopy_launch.sh | 17 +
src/projects/mts/scripts/choose_samples.py | 61 +
src/projects/mts/scripts/combine_contigs.py | 28 +
src/projects/mts/scripts/common.py | 121 +
src/projects/mts/scripts/filter_nucmer.py | 54 +
src/projects/mts/scripts/gather_stats.py | 28 +
src/projects/mts/scripts/gen_samples.py | 96 +
src/projects/mts/scripts/make_input.py | 53 +
src/projects/mts/scripts/make_points_matrix.py | 35 +
src/projects/mts/scripts/parse_output.py | 58 +
src/projects/mts/scripts/pca.R | 77 +
src/projects/mts/scripts/ref_stats.sh | 63 +
src/projects/mts/scripts/split_bins.py | 30 +
src/projects/mts/stats.cpp | 194 ++
src/projects/mts/test.py | 205 ++
src/projects/mts/visualization.hpp | 66 +
src/projects/online_vis/CMakeLists.txt | 6 +-
src/projects/online_vis/debruijn_environment.hpp | 6 +-
.../drawing_commands/draw_contig_command.hpp | 2 +-
.../drawing_commands/draw_missasemblies.hpp | 4 +-
.../drawing_commands/draw_polymorphic_regions.hpp | 17 +-
.../drawing_commands/draw_poorly_assembled.hpp | 6 +-
.../drawing_commands/draw_position_command.hpp | 4 +-
.../drawing_commands/drawing_command.hpp | 8 +-
.../drawing_commands/show_position_command.hpp | 4 +-
src/projects/online_vis/environment.hpp | 6 +-
src/projects/online_vis/main.cpp | 10 +-
src/projects/online_vis/online_visualizer.hpp | 2 +-
.../position_commands/fill_position_command.hpp | 2 +-
src/projects/online_vis/processing_commands.hpp | 4 +-
src/projects/online_vis/standard_vis.hpp | 2 +-
.../junction_sequence_command.hpp | 4 +-
.../statistics_commands/print_contigs_stats.hpp | 2 +-
src/projects/online_vis/vis_logger.hpp | 6 +-
src/projects/scaffold_correction/CMakeLists.txt | 2 +-
src/projects/scaffold_correction/main.cpp | 15 +-
.../scaffold_correction/scaffold_correction.hpp | 17 +-
src/projects/spades/CMakeLists.txt | 10 +-
src/projects/spades/chromosome_removal.cpp | 45 +-
src/projects/spades/chromosome_removal.hpp | 3 +-
src/projects/spades/contig_output_stage.cpp | 55 +
src/projects/spades/contig_output_stage.hpp | 29 +
src/projects/spades/distance_estimation.cpp | 8 +-
src/projects/spades/gap_closer.cpp | 146 +-
src/projects/spades/gap_closing.hpp | 74 +
src/projects/spades/hybrid_aligning.cpp | 462 ++++
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 | 27 +-
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
truspades_manual.html | 2 +-
821 files changed, 70900 insertions(+), 58618 deletions(-)
diff --cc debian/changelog
index 6e80078,8509830..ddebb28
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,10 -1,34 +1,41 @@@
+ spades (3.10.1+dfsg-3) unstable; urgency=medium
+
+ * Fix FTBFS with GCC 7.
+ Closes: #853666
+ * Update homepage.
+ * Bump Standards-Version.
+
+ -- Sascha Steinbiss <satta at debian.org> Thu, 10 Aug 2017 16:39:50 +0200
+
+ spades (3.10.1+dfsg-2) unstable; urgency=medium
+
+ * Upload to unstable.
+
+ -- Sascha Steinbiss <satta at debian.org> Sun, 18 Jun 2017 16:31:57 +0000
+
+ spades (3.10.1+dfsg-1) experimental; urgency=medium
+
+ [ Michael R. Crusoe ]
+ * New upstream version 3.10.1+dfsg
+
+ [ Sascha Steinbiss ]
+ * Build for experimental.
+
+ -- Sascha Steinbiss <satta at debian.org> Fri, 21 Apr 2017 17:54:15 +0000
+
+ spades (3.9.1+dfsg-1) unstable; urgency=medium
+
+ * New upstream release.
+
+ -- Sascha Steinbiss <satta at debian.org> Wed, 07 Dec 2016 06:31:19 +0000
+
+spades (3.9.0+dfsg-1~bpo8+1) jessie-backports; urgency=medium
+
+ * Rebuild for jessie-backports.
+ * Switch manpage building back to asciidoctor.
+
+ -- Afif Elghraoui <afif at debian.org> Sat, 30 Jul 2016 19:33:47 -0700
+
spades (3.9.0+dfsg-1) unstable; urgency=medium
* New upstream release.
--
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