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in repository spades.
from edff796 Imported Upstream version 3.8.2+dfsg2
new 4fe3eea Imported Upstream version 3.9.0+dfsg
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Summary of changes:
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 +
.../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(-)
copy ext/src/samtools/examples/ex1.glf =>
configs/debruijn/simplification.info.template (100%)
create mode 100644 ext/include/cxxopts/cxxopts.hpp
copy metaspades.py => rnaspades.py (93%)
create mode 100644 rnaspades_manual.html
delete mode 100644 src/modules/algorithms/path_extend/utils/CMakeLists.txt
delete mode 100644 src/modules/algorithms/path_extend/utils/find_aligns.py
delete mode 100644
src/modules/algorithms/path_extend/utils/find_single_threshold.py
delete mode 100644
src/modules/algorithms/path_extend/utils/paired_info_checker.cpp
delete mode 100644
src/modules/algorithms/path_extend/utils/run_all_parametrs.py
create mode 100644
src/modules/assembly_graph/graph_alignment/edge_index_refiller.cpp
create mode 100644
src/modules/assembly_graph/graph_alignment/edge_index_refiller.hpp
create mode 100644
src/modules/data_structures/indices/kmer_extension_index_builder.hpp
create mode 100644
src/modules/data_structures/indices/perfect_hash_map_builder.hpp
copy src/modules/data_structures/mph_index/{kmer_index.hpp =>
kmer_index_builder.hpp} (53%)
create mode 100644 src/modules/data_structures/mph_index/kmer_index_traits.hpp
create mode 100644 src/projects/mph_test/CMakeLists.txt
create mode 100644 src/projects/mph_test/main.cpp
create mode 100644 src/utils/adt/bf.hpp
create mode 100644 src/utils/adt/hll.hpp
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