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commit 4075290c0340f4ae870adde83029d483c4adcc22 Merge: 56f008a 4fe3eea Author: Sascha Steinbiss <[email protected]> Date: Sun Jul 24 09:47:31 2016 +0000 Merge tag 'upstream/3.9.0+dfsg' Upstream version 3.9.0+dfsg VERSION | 3 +- changelog.html | 8 + configs/debruijn/config.info | 12 +- configs/debruijn/detail_info_printer.info | 2 + configs/debruijn/log.properties | 2 + configs/debruijn/pe_params.info | 12 +- configs/debruijn/rna_mode.info | 50 +- configs/debruijn/simplification.info | 13 + configs/debruijn/simplification.info.template | 0 ext/include/cxxopts/cxxopts.hpp | 1368 ++++++++++++++++++++ ext/include/llvm/Support/MathExtras.h | 1 - ext/src/bamtools/api/internal/io/pbgzf/bgzf.c | 4 +- ext/src/bamtools/api/internal/io/pbgzf/bgzf.h | 4 +- ext/src/llvm/CMakeLists.txt | 3 - manual.html | 80 +- metaspades.py | 57 +- plasmidspades.py | 57 +- metaspades.py => rnaspades.py | 57 +- rnaspades_manual.html | 84 ++ spades.py | 57 +- src/CMakeLists.txt | 9 +- src/cmake/pack.cmake | 6 +- .../algorithms/genome_consistance_checker.cpp | 2 +- src/modules/algorithms/graph_construction.hpp | 9 +- src/modules/algorithms/mismatch_shall_not_pass.hpp | 15 +- .../algorithms/path_extend/extension_chooser.hpp | 60 +- .../algorithms/path_extend/overlap_analysis.hpp | 14 +- .../algorithms/path_extend/path_extend_launch.hpp | 862 +++++++----- .../algorithms/path_extend/path_extender.hpp | 223 +++- src/modules/algorithms/path_extend/path_filter.hpp | 50 +- .../algorithms/path_extend/pe_config_struct.cpp | 67 +- .../algorithms/path_extend/pe_config_struct.hpp | 365 +++--- src/modules/algorithms/path_extend/pe_io.hpp | 13 +- src/modules/algorithms/path_extend/pe_resolver.hpp | 7 +- .../scaffolder2015/extension_chooser2015.hpp | 22 +- .../algorithms/path_extend/utils/CMakeLists.txt | 13 - .../algorithms/path_extend/utils/find_aligns.py | 67 - .../path_extend/utils/find_single_threshold.py | 101 -- .../path_extend/utils/paired_info_checker.cpp | 204 --- .../path_extend/utils/run_all_parametrs.py | 47 - .../erroneous_connection_remover.hpp | 123 ++ .../algorithms/simplification/tip_clipper.hpp | 12 +- src/modules/assembly_graph/CMakeLists.txt | 2 +- .../assembly_graph/graph_alignment/edge_index.hpp | 41 +- .../graph_alignment/edge_index_refiller.cpp | 33 + .../graph_alignment/edge_index_refiller.hpp | 20 + .../assembly_graph/graph_alignment/kmer_mapper.hpp | 5 + .../graph_alignment/pacbio/pac_index.hpp | 82 +- .../graph_alignment/pacbio/pacbio_gap_closer.hpp | 20 +- .../pacbio/pacbio_read_structures.hpp | 12 +- .../graph_alignment/sequence_mapper.hpp | 69 +- .../graph_alignment/sequence_mapper_notifier.hpp | 3 + .../graph_alignment/short_read_mapper.hpp | 2 +- .../graph_support/basic_edge_conditions.hpp | 1 + .../assembly_graph/graph_support/contig_output.hpp | 22 +- .../graph_support/genomic_quality.hpp | 6 +- .../handlers/edges_position_handler.hpp | 6 + src/modules/assembly_graph/paths/mapping_path.hpp | 5 + src/modules/assembly_graph/stats/picture_dump.hpp | 21 + .../debruijn_graph/debruijn_graph_constructor.hpp | 7 - .../debruijn_graph/early_simplification.hpp | 81 +- .../indices/edge_index_builders.hpp | 33 +- .../data_structures/indices/edge_info_updater.hpp | 1 + .../data_structures/indices/edge_multi_index.hpp | 8 +- .../indices/edge_position_index.hpp | 29 +- .../data_structures/indices/key_with_hash.hpp | 38 +- .../indices/kmer_extension_index.hpp | 108 +- .../indices/kmer_extension_index_builder.hpp | 106 ++ .../data_structures/indices/kmer_splitters.hpp | 249 +--- .../data_structures/indices/perfect_hash_map.hpp | 112 +- .../indices/perfect_hash_map_builder.hpp | 102 ++ .../data_structures/mph_index/kmer_index.hpp | 403 +----- .../{kmer_index.hpp => kmer_index_builder.hpp} | 394 ++---- .../mph_index/kmer_index_traits.hpp | 87 ++ src/modules/data_structures/mph_index/mphf.hpp | 2 +- src/modules/data_structures/sequence/rtseq.hpp | 16 +- src/modules/data_structures/sequence/sequence.hpp | 11 + .../data_structures/sequence/simple_seq.hpp | 5 +- src/modules/io/dataset_support/read_converter.hpp | 403 +++--- .../io/reads_io/modifying_reader_wrapper.hpp | 1 + src/modules/io/reads_io/mpmc_bounded.hpp | 27 +- src/modules/io/reads_io/paired_readers.hpp | 1 + src/modules/io/reads_io/read_processor.hpp | 62 +- src/modules/io/reads_io/splitting_wrapper.hpp | 1 + src/modules/math/kmer_coverage_model.cpp | 4 +- src/modules/paired_info/pair_info_improver.hpp | 6 +- src/modules/pipeline/config_struct.cpp | 47 +- src/modules/pipeline/config_struct.hpp | 46 +- src/modules/pipeline/genomic_info_filler.cpp | 2 +- src/modules/pipeline/graph_pack.hpp | 8 +- src/modules/pipeline/library.hpp | 5 +- src/modules/stages/construction.cpp | 9 +- src/modules/stages/simplification.cpp | 87 +- .../graph_simplification.hpp | 258 ++-- .../simplification_settings.hpp | 11 +- src/modules/visualization/position_filler.hpp | 4 +- src/modules/visualization/visualization_utils.hpp | 12 +- src/projects/CMakeLists.txt | 11 +- src/projects/cap/cap_kmer_index.hpp | 11 - src/projects/cap/mosaic.hpp | 2 +- src/projects/hammer/expander.cpp | 8 +- src/projects/hammer/expander.hpp | 3 +- src/projects/hammer/kmer_cluster.cpp | 2 + src/projects/hammer/kmer_data.cpp | 495 +++---- src/projects/ionhammer/hamcluster.hpp | 1 - src/projects/ionhammer/kmer_data.cpp | 121 +- src/projects/ionhammer/read_corrector.hpp | 56 +- src/projects/mph_test/CMakeLists.txt | 15 + src/projects/mph_test/main.cpp | 184 +++ .../online_vis/debruijn_online_visualizer.hpp | 2 +- .../drawing_commands/draw_contig_command.hpp | 12 +- .../drawing_commands/draw_missasemblies.hpp | 25 +- .../drawing_commands/draw_poorly_assembled.hpp | 135 +- .../drawing_commands/drawing_command.hpp | 7 +- .../position_commands/fill_position_command.hpp | 11 +- src/projects/online_vis/processing_commands.hpp | 2 +- src/projects/online_vis/vis_logger.hpp | 6 +- .../scaffold_correction/scaffold_correction.hpp | 1 + src/projects/spades/chromosome_removal.cpp | 2 +- src/projects/spades/distance_estimation.cpp | 5 +- src/projects/spades/gap_closer.cpp | 7 +- src/projects/spades/main.cpp | 1 + src/projects/spades/mismatch_correction.cpp | 8 +- src/projects/spades/pacbio_aligning.cpp | 8 +- src/projects/spades/pair_info_count.cpp | 12 +- src/projects/spades/repeat_resolving.cpp | 35 +- src/projects/truseq_analysis/analysis_pipeline.cpp | 1 + src/spades_pipeline/options_storage.py | 84 +- src/spades_pipeline/spades_logic.py | 54 +- src/utils/adt/bf.hpp | 174 +++ src/utils/adt/hll.hpp | 69 + 131 files changed, 5295 insertions(+), 3576 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
