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 <[email protected]> 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 +- 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.../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 | 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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 <[email protected]> Thu, 10 Aug 2017 16:39:50 +0200 + + spades (3.10.1+dfsg-2) unstable; urgency=medium + + * Upload to unstable. + + -- Sascha Steinbiss <[email protected]> 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 <[email protected]> Fri, 21 Apr 2017 17:54:15 +0000 + + spades (3.9.1+dfsg-1) unstable; urgency=medium + + * New upstream release. + + -- Sascha Steinbiss <[email protected]> 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 <[email protected]> Sat, 30 Jul 2016 19:33:47 -0700 + spades (3.9.0+dfsg-1) unstable; urgency=medium * New upstream release. -- 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
