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commit 7f5afdbd5b5c795862d0062c7de204ad7d92564d Merge: ec8ce0a 34bcf2c Author: Michael R. Crusoe <[email protected]> Date: Wed Apr 19 02:55:47 2017 -0700 Merge tag 'upstream/3.10.1+dfsg' Upstream version 3.10.1+dfsg LICENSE | 2 +- VERSION | 2 +- changelog.html | 27 + configs/debruijn/config.info | 32 +- configs/debruijn/distance_estimation.info | 12 +- configs/debruijn/large_genome_mode.info | 22 + configs/debruijn/log.properties | 6 + configs/debruijn/mda_mode.info | 11 +- configs/debruijn/meta_mode.info | 49 +- configs/debruijn/moleculo_mode.info | 2 + configs/debruijn/path_extend/pe_params.info | 206 -- configs/debruijn/pe_params.info | 56 +- configs/debruijn/rna_mode.info | 31 +- configs/debruijn/simplification.info | 1 + ext/include/btree/btree.h | 138 +- ext/include/btree/btree_container.h | 45 +- ext/include/btree/btree_map.h | 9 + ext/include/btree/safe_btree.h | 32 +- ext/include/btree/safe_btree_map.h | 8 + ext/include/bwa/bntseq.h | 91 + ext/include/bwa/bwa.h | 62 + ext/include/bwa/bwamem.h | 184 ++ ext/include/bwa/bwt.h | 130 + ext/include/bwa/utils.h | 111 + ext/include/cuckoo/LICENSE | 18 + ext/include/cuckoo/city_hasher.hh | 44 + ext/include/cuckoo/cuckoohash_config.hh | 36 + ext/include/cuckoo/cuckoohash_map.hh | 2537 ++++++++++++++++++++ ext/include/cuckoo/cuckoohash_util.hh | 136 ++ ext/include/cuckoo/libcuckoo_lazy_array.hh | 202 ++ ext/include/llvm/Support/MathExtras.h | 1 + ext/src/CMakeLists.txt | 4 +- ext/src/getopt_pp/CMakeLists.txt | 5 + ext/{include => src}/getopt_pp/getopt_pp.cpp | 2 +- ext/src/llvm/CMakeLists.txt | 3 + manual.html | 105 +- metaspades.py | 102 +- plasmidspades.py | 102 +- rnaspades.py | 102 +- rnaspades_manual.html | 21 +- spades.py | 102 +- spades_compile.sh | 2 +- src/CMakeLists.txt | 6 +- src/cmake/options.cmake | 3 + src/cmake/pack.cmake | 4 +- src/common/CMakeLists.txt | 22 + src/{utils => common}/adt/array_vector.hpp | 0 src/{utils => common}/adt/bag.hpp | 2 +- src/{utils => common}/adt/bf.hpp | 0 src/{utils => common}/adt/chained_iterator.hpp | 0 src/{utils => common}/adt/concurrent_dsu.hpp | 2 +- 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.../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 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.../visualization}/graph_print_utils.hpp | 9 +- .../visualization/graph_printer.hpp | 74 +- .../visualization/position_filler.hpp | 47 +- .../visualization/printing_parameter_storage.hpp | 21 +- .../visualization/vertex_linker.hpp | 19 +- .../visualization/visualization.hpp | 0 src/common/visualization/visualization_utils.hpp | 223 ++ .../visualization/visualizers.hpp | 97 +- src/modules/CMakeLists.txt | 24 - .../algorithms/path_extend/next_path_searcher.hpp | 1031 -------- .../algorithms/path_extend/path_extend_launch.hpp | 1257 ---------- src/modules/algorithms/path_extend/pe_io.hpp | 290 --- .../scaffolder2015/connection_condition2015.cpp | 144 -- .../scaffolder2015/connection_condition2015.hpp | 90 - .../scaffolder2015/extension_chooser2015.hpp | 59 - .../scaffolder2015/scaffold_graph_visualizer.hpp | 73 - .../algorithms/path_extend/weight_counter.hpp | 544 ----- .../simplification/complex_tip_clipper.hpp | 158 -- .../assembly_graph/components/graph_component.hpp | 198 -- .../graph_alignment/pacbio/pacbio_gap_closer.hpp | 396 --- .../graph_support/graph_processing_algorithm.hpp | 262 -- .../graph_support/parallel_processing.hpp | 290 --- .../graph_support/scaff_supplementary.cpp | 66 - .../graph_support/scaff_supplementary.hpp | 77 - src/modules/assembly_graph/paths/path_utils.hpp | 128 - .../data_structures/sequence/CMakeLists.txt | 10 - .../data_structures/sequence/genome_storage.hpp | 33 - src/modules/dev_support/CMakeLists.txt | 13 - src/modules/dev_support/func.hpp | 69 - src/modules/io/dataset_support/dataset_readers.hpp | 122 - src/modules/io/reads_io/binary_streams.hpp | 357 --- src/modules/io/reads_io/cutting_reader_wrapper.hpp | 135 -- src/modules/io/reads_io/easy_reader.hpp | 122 - src/modules/io/reads_io/is_corrupting_wrapper.hpp | 33 - src/modules/paired_info/bwa_pair_info_filler.cpp | 408 ---- src/modules/paired_info/bwa_pair_info_filler.hpp | 253 -- src/modules/paired_info/pair_info_filler.hpp | 119 - .../graph_simplification.hpp | 1034 -------- src/modules/visualization/visualization_utils.hpp | 210 -- src/projects/CMakeLists.txt | 2 +- src/projects/cap/assembly_compare.hpp | 22 +- src/projects/cap/assembly_problem_detection.hpp | 8 +- src/projects/cap/cap_commands.hpp | 4 +- src/projects/cap/cap_environment.hpp | 4 +- src/projects/cap/cap_environment_manager.hpp | 2 +- src/projects/cap/cap_kmer_index.hpp | 8 +- src/projects/cap/cap_logger.hpp | 2 +- src/projects/cap/colored_graph_construction.hpp | 10 +- src/projects/cap/coloring.hpp | 25 +- src/projects/cap/compare_standard.hpp | 26 +- src/projects/cap/comparison_utils.hpp | 16 +- src/projects/cap/coordinates_handler.hpp | 4 +- src/projects/cap/deprecated/tools_deprecated.cpp | 4 +- src/projects/cap/diff_masking.hpp | 10 +- src/projects/cap/gene_analysis.hpp | 4 +- src/projects/cap/genome_correction.hpp | 8 +- src/projects/cap/junk_cropping_reader.hpp | 4 +- src/projects/cap/longseq.hpp | 6 +- src/projects/cap/main.cpp | 8 +- src/projects/cap/mosaic.hpp | 20 +- src/projects/cap/repeat_masking.hpp | 8 +- src/projects/cap/serialization.hpp | 2 +- src/projects/cap/simple_inversion_finder.hpp | 8 +- src/projects/cap/stats.hpp | 38 +- src/projects/cap/tools.cpp | 2 +- src/projects/cap/untangling.hpp | 4 +- src/projects/cap/visualization.hpp | 28 +- src/projects/cclean/CMakeLists.txt | 30 + src/projects/cclean/adapter_index.cpp | 50 + src/projects/cclean/adapter_index.hpp | 61 + src/projects/cclean/additional.cpp | 69 + src/projects/cclean/brute_force_clean.cpp | 97 + src/projects/cclean/brute_force_clean.hpp | 72 + .../cclean/comparator.hpp} | 20 +- src/projects/cclean/config_struct_cclean.cpp | 44 + src/projects/cclean/config_struct_cclean.hpp | 42 + src/projects/cclean/job_wrappers.cpp | 97 + src/projects/cclean/job_wrappers.hpp | 73 + src/projects/cclean/main.cpp | 86 + src/projects/cclean/output.cpp | 82 + src/projects/cclean/output.hpp | 49 + src/projects/cclean/running_modes.cpp | 268 +++ src/projects/cclean/running_modes.hpp | 93 + src/projects/cclean/utils.cpp | 136 ++ src/projects/cclean/utils.hpp | 58 + .../{hammer => cclean}/valid_kmer_generator.hpp | 32 +- src/projects/corrector/CMakeLists.txt | 2 +- src/projects/corrector/config_struct.cpp | 2 +- src/projects/corrector/contig_processor.cpp | 8 +- src/projects/corrector/contig_processor.hpp | 6 +- src/projects/corrector/dataset_processor.cpp | 10 +- src/projects/corrector/dataset_processor.hpp | 6 +- .../corrector/interesting_pos_processor.cpp | 2 +- src/projects/corrector/main.cpp | 4 +- src/projects/dipspades/CMakeLists.txt | 6 +- .../consensus_contigs_constructor.hpp | 4 +- .../contig_correctors/close_gaps_corrector.hpp | 2 +- src/projects/dipspades/dipspades.hpp | 4 +- src/projects/dipspades/dipspades_config.cpp | 2 +- .../conservative_regions_searcher.hpp | 4 +- .../dipspades/kmer_gluing/equal_sequence_gluer.hpp | 2 +- src/projects/dipspades/main.cpp | 10 +- .../bulge_paths_searcher.hpp | 2 +- .../complex_bulge_remover.hpp | 2 +- .../polymorphic_bulge_remover.hpp | 8 +- src/projects/dipspades/utils/edge_gluer.hpp | 2 +- src/projects/dipspades/utils/path_routines.hpp | 5 +- src/projects/hammer/CMakeLists.txt | 2 +- src/projects/hammer/config_struct_hammer.cpp | 2 +- src/projects/hammer/hamcluster.cpp | 4 +- src/projects/hammer/hamcluster.hpp | 6 +- src/projects/hammer/hammer_tools.cpp | 4 +- src/projects/hammer/hammer_tools.hpp | 6 +- src/projects/hammer/kmer_cluster.cpp | 4 +- src/projects/hammer/kmer_data.cpp | 14 +- src/projects/hammer/kmer_data.hpp | 4 +- src/projects/hammer/kmer_stat.hpp | 4 +- src/projects/hammer/main.cpp | 14 +- src/projects/hammer/parallel_radix_sort.hpp | 2 +- src/projects/hammer/quake_correct/bithash.cpp | 2 +- src/projects/hammer/quake_count/quake_count.cpp | 2 +- src/projects/hammer/quake_count/quake_count_17.cpp | 2 +- src/projects/hammer/quake_count/quake_count_19.cpp | 2 +- src/projects/hammer/quake_count/quake_count_21.cpp | 2 +- src/projects/hammer/quake_count/quake_count_25.cpp | 2 +- src/projects/hammer/quake_count/quake_count_29.cpp | 2 +- src/projects/hammer/quake_count/quake_count_33.cpp | 2 +- src/projects/hammer/quake_count/quake_count_37.cpp | 2 +- src/projects/hammer/quake_count/quake_count_45.cpp | 2 +- src/projects/hammer/quake_count/quake_count_55.cpp | 2 +- src/projects/hammer/quake_count/quake_count_65.cpp | 2 +- src/projects/hammer/quake_count/quake_count_75.cpp | 2 +- .../hammer/quake_count/valid_kmer_generator.hpp | 2 +- src/projects/hammer/quake_enhanced/count.cpp | 2 +- src/projects/hammer/quake_enhanced/count/count.cpp | 2 +- .../quake_enhanced/filter_trusted_enh/main.cpp | 2 +- src/projects/hammer/valid_kmer_generator.hpp | 2 +- src/projects/ionhammer/CMakeLists.txt | 2 +- src/projects/ionhammer/HSeq.hpp | 2 +- src/projects/ionhammer/config_struct.cpp | 2 +- src/projects/ionhammer/err_helper_table.cpp | 2 +- src/projects/ionhammer/err_helper_table.hpp | 2 +- src/projects/ionhammer/expander.cpp | 2 +- src/projects/ionhammer/hamcluster.cpp | 4 +- src/projects/ionhammer/hamcluster.hpp | 4 +- src/projects/ionhammer/kmer_data.cpp | 10 +- src/projects/ionhammer/kmer_data.hpp | 2 +- src/projects/ionhammer/main.cpp | 20 +- src/projects/ionhammer/read_corrector.hpp | 2 +- src/projects/ionhammer/subcluster.cpp | 2 +- src/projects/mph_test/CMakeLists.txt | 2 +- src/projects/mph_test/main.cpp | 27 +- src/projects/mts/CMakeLists.txt | 57 + src/projects/mts/Common.snake | 69 + src/projects/mts/README | 21 + src/projects/mts/Snakefile | 175 ++ src/projects/mts/Stats.snake | 270 +++ src/projects/mts/annotation.hpp | 310 +++ src/projects/mts/config.yaml | 10 + src/projects/mts/contig_abundance.cpp | 176 ++ src/projects/mts/contig_abundance.hpp | 143 ++ src/projects/mts/contig_abundance_counter.cpp | 101 + src/projects/mts/formats.hpp | 29 + src/projects/mts/kmc_api/kmc_file.cpp | 1093 +++++++++ src/projects/mts/kmc_api/kmc_file.h | 141 ++ src/projects/mts/kmc_api/kmer_api.cpp | 48 + src/projects/mts/kmc_api/kmer_api.h | 596 +++++ src/projects/mts/kmc_api/kmer_defs.h | 54 + src/projects/mts/kmc_api/mmer.cpp | 49 + src/projects/mts/kmc_api/mmer.h | 182 ++ src/projects/mts/kmc_api/stdafx.h | 4 + src/projects/mts/kmer_multiplicity_counter.cpp | 256 ++ src/projects/mts/log.properties | 10 + src/projects/mts/logger.hpp | 11 + src/projects/mts/mts.py | 73 + src/projects/mts/prop_binning.cpp | 128 + src/projects/mts/propagate.cpp | 331 +++ src/projects/mts/propagate.hpp | 29 + src/projects/mts/read_binning.cpp | 90 + src/projects/mts/read_binning.hpp | 92 + .../empty.cpp => projects/mts/scripts/__init__.py} | 0 src/projects/mts/scripts/calc_kmers_mpl.py | 38 + src/projects/mts/scripts/canopy_launch.sh | 17 + src/projects/mts/scripts/choose_samples.py | 61 + src/projects/mts/scripts/combine_contigs.py | 28 + src/projects/mts/scripts/common.py | 121 + src/projects/mts/scripts/filter_nucmer.py | 54 + src/projects/mts/scripts/gather_stats.py | 28 + src/projects/mts/scripts/gen_samples.py | 96 + src/projects/mts/scripts/make_input.py | 53 + src/projects/mts/scripts/make_points_matrix.py | 35 + src/projects/mts/scripts/parse_output.py | 58 + src/projects/mts/scripts/pca.R | 77 + src/projects/mts/scripts/ref_stats.sh | 63 + src/projects/mts/scripts/split_bins.py | 30 + src/projects/mts/stats.cpp | 194 ++ src/projects/mts/test.py | 205 ++ src/projects/mts/visualization.hpp | 66 + src/projects/online_vis/CMakeLists.txt | 6 +- src/projects/online_vis/debruijn_environment.hpp | 6 +- .../drawing_commands/draw_contig_command.hpp | 2 +- .../drawing_commands/draw_missasemblies.hpp | 4 +- .../drawing_commands/draw_polymorphic_regions.hpp | 17 +- .../drawing_commands/draw_poorly_assembled.hpp | 6 +- .../drawing_commands/draw_position_command.hpp | 4 +- .../drawing_commands/drawing_command.hpp | 8 +- .../drawing_commands/show_position_command.hpp | 4 +- src/projects/online_vis/environment.hpp | 6 +- src/projects/online_vis/main.cpp | 10 +- src/projects/online_vis/online_visualizer.hpp | 2 +- .../position_commands/fill_position_command.hpp | 2 +- src/projects/online_vis/processing_commands.hpp | 4 +- src/projects/online_vis/standard_vis.hpp | 2 +- .../junction_sequence_command.hpp | 4 +- .../statistics_commands/print_contigs_stats.hpp | 2 +- src/projects/online_vis/vis_logger.hpp | 6 +- src/projects/scaffold_correction/CMakeLists.txt | 2 +- src/projects/scaffold_correction/main.cpp | 15 +- .../scaffold_correction/scaffold_correction.hpp | 17 +- src/projects/spades/CMakeLists.txt | 10 +- src/projects/spades/chromosome_removal.cpp | 45 +- src/projects/spades/chromosome_removal.hpp | 3 +- src/projects/spades/contig_output_stage.cpp | 55 + src/projects/spades/contig_output_stage.hpp | 29 + src/projects/spades/distance_estimation.cpp | 8 +- src/projects/spades/gap_closer.cpp | 146 +- src/projects/spades/gap_closing.hpp | 74 + src/projects/spades/hybrid_aligning.cpp | 462 ++++ .../{pacbio_aligning.hpp => hybrid_aligning.hpp} | 6 +- src/projects/spades/hybrid_gap_closer.hpp | 743 ++++++ src/projects/spades/launch.hpp | 69 +- src/projects/spades/main.cpp | 8 +- src/projects/spades/mismatch_correction.cpp | 4 +- src/projects/spades/pacbio_aligning.cpp | 185 -- src/projects/spades/pair_info_count.cpp | 409 ++-- src/projects/spades/repeat_resolving.cpp | 60 +- src/projects/spades/repeat_resolving.hpp | 12 - src/projects/spades/second_phase_setup.cpp | 5 +- src/projects/spades/second_phase_setup.hpp | 7 +- src/projects/spades/series_analysis.hpp | 323 +++ .../truseq_analysis/AlignmentAnalyserNew.cpp | 4 +- .../truseq_analysis/AlignmentAnalyserNew.hpp | 2 +- src/projects/truseq_analysis/CMakeLists.txt | 2 +- .../truseq_analysis/alignment_analyser.cpp | 2 +- .../truseq_analysis/alignment_analyser.hpp | 4 +- src/projects/truseq_analysis/analysis_pipeline.cpp | 6 +- src/projects/truseq_analysis/analysis_pipeline.hpp | 2 +- .../truseq_analysis/consistent_mapping.cpp | 2 +- src/projects/truseq_analysis/main.cpp | 8 +- src/spades_pipeline/corrector_logic.py | 6 +- src/spades_pipeline/hammer_logic.py | 2 + src/spades_pipeline/options_storage.py | 19 +- src/spades_pipeline/spades_logic.py | 16 +- src/spades_pipeline/support.py | 21 + test_dataset_plasmid/pl1.fq.gz | Bin 0 -> 68202 bytes test_dataset_plasmid/pl2.fq.gz | Bin 0 -> 68276 bytes 602 files changed, 25877 insertions(+), 13974 deletions(-) -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
