[med-svn] [spades] branch master updated (98c1383 -> 49633eb)
Sascha Steinbiss
satta at debian.org
Fri Nov 17 16:16:47 UTC 2017
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch master
in repository spades.
from 98c1383 Added references to registries.
new 7c4e71e New upstream version 3.11.1+dfsg
new 49633eb Update upstream source from tag 'upstream/3.11.1+dfsg'
The 2 revisions listed above as "new" are entirely new to this
repository and will be described in separate emails. The revisions
listed as "adds" were already present in the repository and have only
been added to this reference.
Summary of changes:
LICENSE | 7 +-
README | 9 +-
VERSION | 2 +-
changelog.html | 33 +-
configs/corrector/corrector.info | 3 +-
configs/corrector/log.properties | 2 +
.../{careful_mode.info => careful_mda_mode.info} | 14 +-
configs/debruijn/careful_mode.info | 12 +-
configs/debruijn/config.info | 25 +-
configs/debruijn/log.properties | 2 +
configs/debruijn/mda_mode.info | 2 +-
configs/debruijn/meta_mode.info | 31 +-
configs/debruijn/moleculo_mode.info | 6 +-
configs/debruijn/pe_params.info | 35 +-
configs/debruijn/rna_fast_mode.info | 12 +
configs/debruijn/rna_mode.info | 80 +-
configs/debruijn/simplification.info | 36 +-
configs/debruijn/toy.info | 4 +
configs/debruijn/toy.yaml | 4 +
ext/include/ConsensusCore/Feature.hpp | 166 --
ext/include/ConsensusCore/Features.hpp | 68 -
.../ConsensusCore/Matrix/SparseMatrix-inl.hpp | 1 -
ext/include/ConsensusCore/Poa/PoaGraph.hpp | 4 +-
ext/include/ConsensusCore/Version.hpp | 1 -
ext/include/boomphf/BooPHF.h | 1422 +++++++++++++
ext/include/llvm/ADT/IntrusiveRefCntPtr.h | 2 +-
ext/include/llvm/Support/MathExtras.h | 46 +
ext/include/llvm/Support/TrailingObjects.h | 401 ++++
ext/src/ConsensusCore/CMakeLists.txt | 2 -
ext/src/ConsensusCore/Feature.cpp | 64 -
ext/src/ConsensusCore/Features.cpp | 51 -
ext/src/ConsensusCore/Matrix/DenseMatrix.cpp | 6 +-
ext/src/ConsensusCore/Matrix/SparseMatrix.cpp | 4 +-
ext/src/ConsensusCore/Poa/PoaConsensus.cpp | 7 +-
ext/src/ConsensusCore/Poa/PoaGraph.cpp | 33 +-
ext/src/ConsensusCore/Version.cpp | 2 -
manual.html | 88 +-
metaspades.py | 81 +-
plasmidspades.py | 81 +-
rnaspades.py | 81 +-
rnaspades_manual.html | 48 +-
spades.py | 81 +-
src/CMakeLists.txt | 5 +
src/cmake/options.cmake | 9 +
src/cmake/pack.cmake | 4 +-
src/common/CMakeLists.txt | 7 +-
src/common/adt/array_vector.hpp | 327 +--
src/common/adt/bag.hpp | 16 +-
src/common/adt/bf.hpp | 285 +--
src/common/adt/chained_iterator.hpp | 4 +-
src/common/adt/concurrent_dsu.hpp | 15 +-
src/common/adt/filter_iterator.hpp | 32 +-
src/common/adt/flat_map.hpp | 59 +-
src/common/adt/flat_set.hpp | 40 +-
src/common/adt/hll.hpp | 31 +-
src/common/adt/iterator_range.hpp | 11 +-
src/common/adt/kmer_hash_vector.hpp | 370 ----
src/common/adt/kmer_vector.hpp | 22 +-
src/common/adt/loser_tree.hpp | 29 +-
src/common/adt/parallel_seq_vector.hpp | 110 -
src/common/adt/parallel_unordered_map.hpp | 137 --
src/common/adt/pointer_iterator.hpp | 4 +
src/common/adt/queue_iterator.hpp | 22 +-
src/common/adt/small_pod_vector.hpp | 6 +-
.../components/connected_component.cpp | 4 +-
.../components/connected_component.hpp | 2 +-
src/common/assembly_graph/components/splitters.hpp | 33 +-
.../construction}/debruijn_graph_constructor.hpp | 367 ++--
.../construction}/early_simplification.hpp | 8 +-
src/common/assembly_graph/core/graph_core.hpp | 30 +-
src/common/assembly_graph/core/graph_iterators.hpp | 13 +-
src/common/assembly_graph/core/order_and_law.hpp | 2 +-
.../assembly_graph/dijkstra/dijkstra_algorithm.hpp | 8 +-
.../assembly_graph/graph_support/contig_output.hpp | 584 +----
.../graph_support/coverage_filling.hpp | 4 +-
.../graph_support/detail_coverage.hpp | 5 +-
.../graph_support/genomic_quality.hpp | 20 +-
.../graph_support/parallel_processing.hpp | 76 +-
.../graph_support/scaff_supplementary.cpp | 46 +-
.../graph_support/scaff_supplementary.hpp | 110 +-
.../handlers/edge_labels_handler.hpp | 2 +-
.../handlers/edges_position_handler.hpp | 30 +-
.../assembly_graph/handlers/id_track_handler.hpp | 31 +-
.../index}/edge_index_builders.hpp | 84 +-
.../index}/edge_info_updater.hpp | 4 +-
.../index}/edge_multi_index.hpp | 8 +-
.../index}/edge_position_index.hpp | 22 +-
.../assembly_graph/paths/bidirectional_path.hpp | 766 ++-----
.../paths/bidirectional_path_container.hpp | 210 ++
.../bidirectional_path_output.cpp | 71 +-
.../bidirectional_path_output.hpp | 274 ++-
.../paths/bidirectional_path_io/io_support.cpp | 100 +-
.../paths/bidirectional_path_io/io_support.hpp | 81 +-
src/common/assembly_graph/paths/mapping_path.hpp | 227 +-
src/common/assembly_graph/paths/path_processor.hpp | 17 +-
src/common/assembly_graph/stats/picture_dump.hpp | 47 +-
src/common/assembly_graph/stats/statistics.hpp | 7 +-
src/common/io/dataset_support/dataset_readers.hpp | 2 +-
src/common/io/dataset_support/read_converter.hpp | 4 +-
src/common/io/kmers/kmer_iterator.hpp | 2 +-
src/common/io/kmers/mmapped_reader.hpp | 9 +-
src/common/io/kmers/mmapped_writer.hpp | 14 +-
src/common/io/reads/binary_converter.hpp | 2 +-
src/common/io/reads/binary_streams.hpp | 4 +-
src/common/io/reads/fasta_fastq_gz_parser.hpp | 5 +
src/common/io/reads/file_reader.hpp | 4 +-
src/common/io/reads/ireadstream.hpp | 4 +
src/common/io/reads/osequencestream.hpp | 318 +--
src/common/io/reads/paired_read.hpp | 5 -
src/common/io/reads/read.hpp | 2 +-
src/common/io/reads/read_processor.hpp | 2 +-
src/common/io/reads/sequence_reader.hpp | 2 +-
src/common/io/reads/single_read.hpp | 22 +-
src/common/io/reads/wrapper_collection.hpp | 2 +-
src/common/{utils => math}/log.hpp | 0
src/common/modules/alignment/bwa_index.cpp | 10 +-
src/common/modules/alignment/edge_index.hpp | 8 +-
.../modules/alignment/edge_index_refiller.cpp | 4 +-
src/common/modules/alignment/kmer_mapper.hpp | 4 +-
.../modules/alignment/kmer_mapper_logger.hpp | 2 +-
src/common/modules/alignment/pacbio/pac_index.hpp | 281 ++-
.../alignment/pacbio/pacbio_read_structures.hpp | 60 +-
src/common/modules/alignment/rna/ss_coverage.hpp | 61 +
.../modules/alignment/rna/ss_coverage_filler.hpp | 62 +
src/common/modules/alignment/sequence_mapper.hpp | 5 +-
.../modules/alignment/sequence_mapper_notifier.hpp | 17 +-
src/common/modules/alignment/short_read_mapper.hpp | 2 +-
.../coverage_model/CMakeLists.txt | 0
.../coverage_model/kmer_coverage_model.cpp | 2 -
.../coverage_model/kmer_coverage_model.hpp | 2 -
src/common/modules/genome_consistance_checker.cpp | 610 ++++--
src/common/modules/genome_consistance_checker.hpp | 221 +-
src/common/modules/graph_construction.hpp | 36 +-
src/common/modules/graph_read_correction.hpp | 4 +-
.../modules/path_extend/extension_chooser.hpp | 269 ++-
src/common/modules/path_extend/loop_traverser.hpp | 127 +-
.../modules/path_extend/overlap_analysis.hpp | 4 +-
src/common/modules/path_extend/path_extender.hpp | 1457 ++++++-------
src/common/modules/path_extend/path_filter.hpp | 163 +-
src/common/modules/path_extend/path_visualizer.hpp | 4 +-
.../modules/path_extend/pe_config_struct.cpp | 66 +-
.../modules/path_extend/pe_config_struct.hpp | 29 +-
src/common/modules/path_extend/pe_resolver.hpp | 700 ++----
src/common/modules/path_extend/pe_utils.hpp | 156 +-
.../path_extend/pipeline/extenders_logic.cpp | 137 +-
.../path_extend/pipeline/extenders_logic.hpp | 40 +-
.../path_extend/pipeline/launch_support.cpp | 11 +-
.../path_extend/pipeline/launch_support.hpp | 18 +-
.../modules/path_extend/pipeline/launcher.cpp | 288 ++-
.../modules/path_extend/pipeline/launcher.hpp | 40 +-
.../scaffolder2015/connection_condition2015.cpp | 4 +-
.../scaffolder2015/connection_condition2015.hpp | 2 +-
.../scaffolder2015/extension_chooser2015.hpp | 2 +-
.../path_extend/scaffolder2015/path_polisher.cpp | 371 ++--
.../path_extend/scaffolder2015/path_polisher.hpp | 120 +-
.../path_extend/scaffolder2015/scaffold_graph.hpp | 2 +-
.../scaffolder2015/scaffold_graph_visualizer.cpp | 12 +-
src/common/modules/path_extend/weight_counter.hpp | 83 +-
.../modules/simplification/bulge_remover.hpp | 190 +-
src/common/modules/simplification/cleaner.hpp | 6 +
.../simplification/complex_bulge_remover.hpp | 46 +-
.../modules/simplification/complex_tip_clipper.hpp | 2 +-
src/common/modules/simplification/compressor.hpp | 2 +-
.../simplification/dominated_set_finder.hpp | 10 +-
.../modules/simplification/ec_threshold_finder.hpp | 8 +-
.../erroneous_connection_remover.hpp | 14 +-
.../parallel_simplification_algorithms.hpp | 86 +-
.../simplification/relative_coverage_remover.hpp | 14 +-
src/common/modules/simplification/tip_clipper.hpp | 14 +-
.../coverage_model => paired_info}/CMakeLists.txt | 9 +-
src/common/paired_info/distance_estimation.cpp | 176 ++
src/common/paired_info/distance_estimation.hpp | 227 +-
src/common/paired_info/histogram.hpp | 4 +-
src/common/paired_info/paired_info.hpp | 2 +-
.../paired_info/smoothing_distance_estimation.cpp | 185 ++
.../paired_info/smoothing_distance_estimation.hpp | 198 +-
src/common/paired_info/split_path_constructor.hpp | 2 +-
.../paired_info/weighted_distance_estimation.cpp | 63 +
.../paired_info/weighted_distance_estimation.hpp | 69 +-
src/common/paired_info/weights.hpp | 3 +-
src/common/pipeline/config_common.hpp | 8 +-
src/common/pipeline/config_struct.cpp | 58 +-
src/common/pipeline/config_struct.hpp | 31 +-
src/common/pipeline/genomic_info_filler.cpp | 10 +-
src/common/pipeline/graph_pack.hpp | 17 +-
src/common/pipeline/graphio.hpp | 29 +-
src/common/pipeline/library.cpp | 2 +-
src/common/pipeline/library.hpp | 10 +-
src/common/pipeline/library.inl | 2 +-
src/common/pipeline/stage.cpp | 4 +-
src/common/sequence/genome_storage.hpp | 67 +-
src/common/{utils => sequence}/levenshtein.hpp | 8 +-
src/common/{utils => sequence}/range.hpp | 7 +-
src/common/sequence/rtseq.hpp | 17 +-
src/common/sequence/seq.hpp | 10 +-
src/common/sequence/sequence.hpp | 121 +-
src/common/sequence/sequence_tools.hpp | 4 +-
src/common/sequence/simple_seq.hpp | 2 +-
src/common/stages/construction.cpp | 2 +-
src/common/stages/simplification.cpp | 47 +-
.../graph_simplification.hpp | 49 +-
.../simplification_pipeline/rna_simplification.hpp | 9 +-
src/common/utils/CMakeLists.txt | 4 +-
src/common/utils/autocompletion.cpp | 2 +-
src/common/utils/autocompletion.hpp | 2 +-
src/common/utils/cpp_utils.hpp | 5 +
.../kmer_extension_index.hpp | 53 +-
.../kmer_extension_index_builder.hpp | 9 +-
src/common/utils/{ => filesystem}/copy_file.cpp | 25 +-
src/common/utils/{ => filesystem}/copy_file.hpp | 10 +-
src/common/utils/{ => filesystem}/file_limit.hpp | 4 +
src/common/utils/{ => filesystem}/path_helper.cpp | 11 +-
src/common/utils/{ => filesystem}/path_helper.hpp | 22 +-
src/common/utils/indices/editable_index.hpp | 270 ---
src/common/utils/indices/kmer_splitters.hpp | 317 ---
.../common/utils/kmer_mph/1.cpp | 0
.../utils/{mph_index => kmer_mph}/CMakeLists.txt | 2 +-
.../utils/{mph_index => kmer_mph}/kmer_index.hpp | 33 +-
.../{mph_index => kmer_mph}/kmer_index_builder.hpp | 216 +-
.../{mph_index => kmer_mph}/kmer_index_traits.hpp | 28 +-
src/common/utils/kmer_mph/kmer_splitters.hpp | 394 ++++
src/common/utils/logger/log_writers.hpp | 44 +-
src/common/utils/logger/logger.hpp | 9 +-
src/common/utils/logger/logger_impl.cpp | 19 +-
src/common/utils/md5.h | 4 +
src/common/utils/mph_index/base_hash.hpp | 293 ---
src/common/utils/mph_index/bitpair_vector.cpp | 77 -
src/common/utils/mph_index/bitpair_vector.hpp | 27 -
src/common/utils/mph_index/common.hpp | 66 -
src/common/utils/mph_index/emphf_config.hpp | 6 -
src/common/utils/mph_index/hypergraph.hpp | 137 --
.../utils/mph_index/hypergraph_sorter_seq.hpp | 130 --
src/common/utils/mph_index/mphf.hpp | 136 --
.../utils/mph_index/ranked_bitpair_vector.hpp | 91 -
src/common/utils/{ => parallel}/openmp_wrapper.h | 0
.../utils/{ => parallel}/parallel_wrapper.hpp | 0
src/common/utils/{ => perf}/memory.hpp | 11 +-
src/common/utils/{ => perf}/memory_limit.hpp | 7 +-
src/common/utils/{ => perf}/perfcounter.hpp | 70 +-
.../utils/{indices => ph_map}/key_with_hash.hpp | 2 +-
.../utils/{indices => ph_map}/perfect_hash_map.hpp | 12 +-
.../perfect_hash_map_builder.hpp | 15 +-
.../utils/{indices => ph_map}/storing_traits.hpp | 23 +-
src/common/utils/{indices => ph_map}/values.hpp | 2 +-
src/common/utils/segfault_handler.hpp | 5 +
src/common/utils/simple_tools.hpp | 189 --
src/common/utils/stacktrace.hpp | 11 +-
src/common/utils/standard_base.hpp | 10 +-
src/common/utils/stl_utils.hpp | 141 ++
src/common/utils/verify.hpp | 7 +-
src/common/visualization/graph_labeler.hpp | 12 +-
src/common/visualization/graph_print_utils.hpp | 8 +-
src/common/visualization/position_filler.hpp | 50 +-
src/common/visualization/visualization_utils.hpp | 10 +-
src/projects/cap/assembly_compare.hpp | 2 +-
src/projects/cap/assembly_problem_detection.hpp | 6 +-
src/projects/cap/cap_commands.hpp | 8 +-
src/projects/cap/cap_environment_manager.hpp | 2 +-
src/projects/cap/cap_kmer_index.hpp | 4 +-
src/projects/cap/compare_standard.hpp | 4 +-
src/projects/cap/comparison_utils.hpp | 8 +-
src/projects/cap/deprecated/tools_deprecated.cpp | 2 +-
src/projects/cap/diff_masking.hpp | 2 +-
src/projects/cap/gene_analysis.hpp | 14 +-
src/projects/cap/genome_correction.hpp | 8 +-
src/projects/cap/longseq.hpp | 4 +-
src/projects/cap/main.cpp | 4 +-
src/projects/cap/mosaic.hpp | 8 +-
src/projects/cap/repeat_masking.hpp | 8 +-
src/projects/cap/simple_inversion_finder.hpp | 4 +-
src/projects/cap/stats.hpp | 24 +-
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/config_struct.cpp | 3 +-
src/projects/corrector/config_struct.hpp | 1 +
src/projects/corrector/contig_processor.cpp | 32 +-
src/projects/corrector/contig_processor.hpp | 8 +-
src/projects/corrector/dataset_processor.cpp | 34 +-
src/projects/corrector/dataset_processor.hpp | 9 +-
.../corrector/interesting_pos_processor.hpp | 5 +
src/projects/corrector/main.cpp | 25 +-
src/projects/corrector/positional_read.hpp | 7 +-
.../consensus_contigs_constructor.hpp | 10 +-
.../contig_correctors/close_gaps_corrector.hpp | 16 +-
.../equal_path_deletion_correction.hpp | 2 +-
.../contig_correctors/incorrect_contig_remover.hpp | 2 +-
.../iterative_redundant_contigs_remover.hpp | 16 +-
.../contig_correctors/overlap_searcher.hpp | 10 +-
.../contig_correctors/redundant_contig_remover.hpp | 4 +-
.../overlap_graph.hpp | 6 +-
src/projects/dipspades/dipspades.hpp | 20 +-
src/projects/dipspades/dipspades_config.cpp | 4 +-
.../conservative_regions_searcher.hpp | 4 +-
.../haplotype_assembly/haplotype_assembler.hpp | 2 +-
src/projects/dipspades/main.cpp | 22 +-
.../polymorphic_bulge_remover.hpp | 8 +-
src/projects/dipspades/utils/bulge_utils.hpp | 2 +-
src/projects/hammer/config_struct_hammer.cpp | 2 +-
src/projects/hammer/hamcluster.cpp | 14 +-
src/projects/hammer/hamcluster.hpp | 6 +-
src/projects/hammer/hammer_tools.cpp | 2 +-
src/projects/hammer/kmer_cluster.cpp | 20 +-
src/projects/hammer/kmer_data.cpp | 28 +-
src/projects/hammer/kmer_data.hpp | 13 +-
src/projects/hammer/main.cpp | 10 +-
src/projects/hammer/parallel_radix_sort.hpp | 2 +-
src/projects/ionhammer/CMakeLists.txt | 22 +-
src/projects/ionhammer/HSeq.hpp | 230 +-
src/projects/ionhammer/comparator.py | 215 ++
src/projects/ionhammer/config_struct.cpp | 134 +-
src/projects/ionhammer/config_struct.hpp | 37 +-
src/projects/ionhammer/consensus.hpp | 12 +-
src/projects/ionhammer/err_helper_table.cpp | 18 +-
src/projects/ionhammer/err_helper_table.hpp | 50 +-
src/projects/ionhammer/expander.cpp | 60 -
src/projects/ionhammer/expander.hpp | 31 -
src/projects/ionhammer/flow_space_read.hpp | 33 +-
src/projects/ionhammer/gamma_poisson_model.cpp | 16 +
src/projects/ionhammer/gamma_poisson_model.hpp | 869 ++++++++
src/projects/ionhammer/hamcluster.cpp | 219 --
src/projects/ionhammer/hamcluster.hpp | 191 --
src/projects/ionhammer/hamcluster_1.cpp | 5 +
src/projects/ionhammer/hamcluster_1.h | 81 +
src/projects/ionhammer/hkmer.hpp | 34 +-
src/projects/ionhammer/hkmer_distance.hpp | 217 +-
src/projects/ionhammer/io_read_corrector.hpp | 230 ++
src/projects/ionhammer/kmer_data.cpp | 119 +-
src/projects/ionhammer/kmer_data.hpp | 77 +-
src/projects/ionhammer/kmer_evaluator.cpp | 53 +
src/projects/ionhammer/kmer_helpers.cpp | 5 +
src/projects/ionhammer/kmer_helpers.h | 69 +
src/projects/ionhammer/main.cpp | 497 +++--
src/projects/ionhammer/normal_quality_model.cpp | 14 +
src/projects/ionhammer/normal_quality_model.hpp | 490 +++++
src/projects/ionhammer/penalty_estimator.hpp | 326 +++
src/projects/ionhammer/quality_metrics.cpp | 5 +
src/projects/ionhammer/quality_metrics.h | 189 ++
.../ionhammer/quality_thresholds_estimator.cpp | 5 +
.../ionhammer/quality_thresholds_estimator.h | 101 +
src/projects/ionhammer/read_corrector.hpp | 563 +++--
src/projects/ionhammer/read_corrector_new.hpp | 252 +++
.../ionhammer/read_corrector_structs_new.h | 740 +++++++
src/projects/ionhammer/reference.cpp | 1 +
src/projects/ionhammer/reference.h | 59 +
src/projects/ionhammer/subcluster.cpp | 283 ++-
src/projects/ionhammer/subcluster.hpp | 100 +-
src/projects/ionhammer/thread_utils.h | 57 +
src/projects/ionhammer/valid_hkmer_generator.hpp | 130 +-
src/projects/mph_test/main.cpp | 29 +-
src/projects/mts/CMakeLists.txt | 3 +-
src/projects/mts/Common.snake | 98 +-
src/projects/mts/README | 15 +-
src/projects/mts/Reassembly.snake | 74 +
src/projects/mts/Snakefile | 413 ++--
src/projects/mts/Stats.snake | 395 ++--
src/projects/mts/annotation.hpp | 30 +-
src/projects/mts/config.yaml | 34 +-
src/projects/mts/contig_abundance.cpp | 80 +-
src/projects/mts/contig_abundance.hpp | 43 +-
src/projects/mts/contig_abundance_counter.cpp | 61 +-
.../quake_correct => mts/gzstream}/gzstream.C | 6 +-
.../quake_correct => mts/gzstream}/gzstream.h | 7 -
src/projects/mts/kmer_multiplicity_counter.cpp | 14 +-
src/projects/mts/logger.hpp | 2 +-
src/projects/mts/mts.py | 71 +-
src/projects/mts/multirun.py | 84 +
src/projects/mts/prop_binning.cpp | 84 +-
src/projects/mts/propagate.cpp | 120 +-
src/projects/mts/propagate.hpp | 10 +-
src/projects/mts/read_binning.cpp | 74 +-
src/projects/mts/read_binning.hpp | 31 +-
src/projects/mts/scripts/Dataset_analysis.ipynb | 2246 ++++++++++++++++++++
src/projects/mts/scripts/bhtsne.py | 242 +++
src/projects/mts/scripts/bin_profiles.py | 12 +
src/projects/mts/scripts/calc_kmers_mpl.py | 38 -
src/projects/mts/scripts/canopy_launch.sh | 17 -
src/projects/mts/scripts/choose_bins.py | 20 +
src/projects/mts/scripts/choose_samples.py | 115 +-
src/projects/mts/scripts/clusters2csv.py | 22 +
src/projects/mts/scripts/combine_contigs.py | 8 +-
src/projects/mts/scripts/common.py | 63 +-
src/projects/mts/scripts/contig_name_filter.py | 30 +
src/projects/mts/scripts/convert_output.py | 53 +
src/projects/mts/scripts/cut_fasta.py | 45 +
src/projects/mts/scripts/filter_bin.py | 17 +
src/projects/mts/scripts/filter_nucmer.py | 62 +-
src/projects/mts/scripts/gather_stats.py | 84 +-
src/projects/mts/scripts/gen_samples.py | 77 +-
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 | 47 +-
src/projects/mts/scripts/ref_stats.sh | 63 -
src/projects/mts/scripts/run_tsne.py | 239 +++
src/projects/mts/scripts/split_bins.py | 18 +-
src/projects/mts/scripts/validate.pl | 404 ++++
src/projects/mts/stats.cpp | 8 +-
src/projects/mts/test.py | 55 +-
src/projects/mts/visualization.hpp | 4 +-
src/projects/online_vis/debruijn_environment.hpp | 2 +-
.../drawing_commands/draw_missasemblies.hpp | 6 +-
.../draw_part_of_genome_command.hpp | 2 +-
.../drawing_commands/draw_polymorphic_regions.hpp | 4 +-
.../drawing_commands/draw_poorly_assembled.hpp | 6 +-
src/projects/online_vis/errors.hpp | 2 +-
src/projects/online_vis/main.cpp | 14 +-
src/projects/online_vis/online_visualizer.hpp | 6 +-
src/projects/online_vis/setting_commands.hpp | 2 +-
src/projects/scaffold_correction/main.cpp | 20 +-
.../scaffold_correction/scaffold_correction.hpp | 8 +-
src/projects/spades/CMakeLists.txt | 1 +
src/projects/spades/chromosome_removal.cpp | 25 +-
src/projects/spades/chromosome_removal.hpp | 1 -
src/projects/spades/contig_output_stage.cpp | 82 +-
src/projects/spades/contig_output_stage.hpp | 15 +-
src/projects/spades/distance_estimation.cpp | 22 +-
src/projects/spades/gap_closer.cpp | 2 -
src/projects/spades/gap_closing.hpp | 42 +-
src/projects/spades/hybrid_aligning.cpp | 4 +-
src/projects/spades/hybrid_gap_closer.hpp | 174 +-
src/projects/spades/launch.hpp | 11 +-
src/projects/spades/main.cpp | 19 +-
src/projects/spades/pair_info_count.cpp | 145 +-
src/projects/spades/repeat_resolving.cpp | 1 +
src/projects/spades/second_phase_setup.cpp | 4 +-
src/projects/spades/second_phase_setup.hpp | 7 +-
.../{series_analysis.hpp => series_analysis.cpp} | 248 ++-
src/projects/spades/series_analysis.hpp | 306 +--
.../truseq_analysis/AlignmentAnalyserNew.cpp | 1 -
.../truseq_analysis/consistent_mapping.cpp | 3 +-
src/projects/truseq_analysis/consistent_mapping.h | 12 +-
src/projects/truseq_analysis/main.cpp | 16 +-
src/spades_pipeline/CMakeLists.txt | 2 +-
src/spades_pipeline/common/SeqIO.py | 34 +-
.../scripts => spades_pipeline/common}/__init__.py | 0
src/spades_pipeline/corrector_logic.py | 5 +-
src/spades_pipeline/hammer_logic.py | 9 +-
src/spades_pipeline/options_storage.py | 48 +-
src/spades_pipeline/spades_logic.py | 41 +-
src/spades_pipeline/support.py | 64 +-
test_dataset/reference_1K.fa.gz | Bin 534 -> 534 bytes
458 files changed, 20300 insertions(+), 14623 deletions(-)
create mode 100644 configs/corrector/log.properties
copy configs/debruijn/{careful_mode.info => careful_mda_mode.info} (64%)
create mode 100644 configs/debruijn/rna_fast_mode.info
create mode 100644 configs/debruijn/toy.info
create mode 100644 configs/debruijn/toy.yaml
delete mode 100644 ext/include/ConsensusCore/Feature.hpp
delete mode 100644 ext/include/ConsensusCore/Features.hpp
create mode 100644 ext/include/boomphf/BooPHF.h
create mode 100644 ext/include/llvm/Support/TrailingObjects.h
delete mode 100644 ext/src/ConsensusCore/Feature.cpp
delete mode 100644 ext/src/ConsensusCore/Features.cpp
delete mode 100644 src/common/adt/kmer_hash_vector.hpp
delete mode 100644 src/common/adt/parallel_seq_vector.hpp
delete mode 100644 src/common/adt/parallel_unordered_map.hpp
rename src/common/{utils/debruijn_graph => assembly_graph/construction}/debruijn_graph_constructor.hpp (61%)
rename src/common/{utils/debruijn_graph => assembly_graph/construction}/early_simplification.hpp (97%)
rename src/common/{utils/indices => assembly_graph/index}/edge_index_builders.hpp (65%)
rename src/common/{utils/indices => assembly_graph/index}/edge_info_updater.hpp (97%)
rename src/common/{utils/indices => assembly_graph/index}/edge_multi_index.hpp (91%)
rename src/common/{utils/indices => assembly_graph/index}/edge_position_index.hpp (88%)
create mode 100644 src/common/assembly_graph/paths/bidirectional_path_container.hpp
rename src/common/{utils => math}/log.hpp (100%)
create mode 100644 src/common/modules/alignment/rna/ss_coverage.hpp
create mode 100644 src/common/modules/alignment/rna/ss_coverage_filler.hpp
copy src/common/{utils => modules}/coverage_model/CMakeLists.txt (100%)
rename src/common/{utils => modules}/coverage_model/kmer_coverage_model.cpp (99%)
rename src/common/{utils => modules}/coverage_model/kmer_coverage_model.hpp (98%)
rename src/common/{utils/coverage_model => paired_info}/CMakeLists.txt (67%)
create mode 100644 src/common/paired_info/distance_estimation.cpp
create mode 100644 src/common/paired_info/smoothing_distance_estimation.cpp
create mode 100644 src/common/paired_info/weighted_distance_estimation.cpp
rename src/common/{utils => sequence}/levenshtein.hpp (96%)
rename src/common/{utils => sequence}/range.hpp (95%)
rename src/common/utils/{indices => extension_index}/kmer_extension_index.hpp (89%)
rename src/common/utils/{indices => extension_index}/kmer_extension_index_builder.hpp (95%)
rename src/common/utils/{ => filesystem}/copy_file.cpp (87%)
rename src/common/utils/{ => filesystem}/copy_file.hpp (63%)
rename src/common/utils/{ => filesystem}/file_limit.hpp (97%)
rename src/common/utils/{ => filesystem}/path_helper.cpp (97%)
rename src/common/utils/{ => filesystem}/path_helper.hpp (84%)
delete mode 100644 src/common/utils/indices/editable_index.hpp
delete mode 100644 src/common/utils/indices/kmer_splitters.hpp
rename configs/debruijn/simplification.info.template => src/common/utils/kmer_mph/1.cpp (100%)
rename src/common/utils/{mph_index => kmer_mph}/CMakeLists.txt (88%)
rename src/common/utils/{mph_index => kmer_mph}/kmer_index.hpp (80%)
rename src/common/utils/{mph_index => kmer_mph}/kmer_index_builder.hpp (57%)
rename src/common/utils/{mph_index => kmer_mph}/kmer_index_traits.hpp (76%)
create mode 100644 src/common/utils/kmer_mph/kmer_splitters.hpp
delete mode 100644 src/common/utils/mph_index/base_hash.hpp
delete mode 100644 src/common/utils/mph_index/bitpair_vector.cpp
delete mode 100644 src/common/utils/mph_index/bitpair_vector.hpp
delete mode 100644 src/common/utils/mph_index/common.hpp
delete mode 100644 src/common/utils/mph_index/emphf_config.hpp
delete mode 100644 src/common/utils/mph_index/hypergraph.hpp
delete mode 100644 src/common/utils/mph_index/hypergraph_sorter_seq.hpp
delete mode 100644 src/common/utils/mph_index/mphf.hpp
delete mode 100644 src/common/utils/mph_index/ranked_bitpair_vector.hpp
rename src/common/utils/{ => parallel}/openmp_wrapper.h (100%)
rename src/common/utils/{ => parallel}/parallel_wrapper.hpp (100%)
rename src/common/utils/{ => perf}/memory.hpp (91%)
rename src/common/utils/{ => perf}/memory_limit.hpp (97%)
rename src/common/utils/{ => perf}/perfcounter.hpp (64%)
rename src/common/utils/{indices => ph_map}/key_with_hash.hpp (99%)
rename src/common/utils/{indices => ph_map}/perfect_hash_map.hpp (97%)
rename src/common/utils/{indices => ph_map}/perfect_hash_map_builder.hpp (87%)
rename src/common/utils/{indices => ph_map}/storing_traits.hpp (83%)
rename src/common/utils/{indices => ph_map}/values.hpp (98%)
delete mode 100644 src/common/utils/simple_tools.hpp
create mode 100644 src/common/utils/stl_utils.hpp
delete mode 100644 src/projects/cclean/CMakeLists.txt
delete mode 100644 src/projects/cclean/adapter_index.cpp
delete mode 100644 src/projects/cclean/adapter_index.hpp
delete mode 100644 src/projects/cclean/additional.cpp
delete mode 100644 src/projects/cclean/brute_force_clean.cpp
delete mode 100644 src/projects/cclean/brute_force_clean.hpp
delete mode 100644 src/projects/cclean/comparator.hpp
delete mode 100644 src/projects/cclean/config_struct_cclean.cpp
delete mode 100644 src/projects/cclean/config_struct_cclean.hpp
delete mode 100644 src/projects/cclean/job_wrappers.cpp
delete mode 100644 src/projects/cclean/job_wrappers.hpp
delete mode 100644 src/projects/cclean/main.cpp
delete mode 100644 src/projects/cclean/output.cpp
delete mode 100644 src/projects/cclean/output.hpp
delete mode 100644 src/projects/cclean/running_modes.cpp
delete mode 100644 src/projects/cclean/running_modes.hpp
delete mode 100644 src/projects/cclean/utils.cpp
delete mode 100644 src/projects/cclean/utils.hpp
delete mode 100644 src/projects/cclean/valid_kmer_generator.hpp
create mode 100755 src/projects/ionhammer/comparator.py
delete mode 100644 src/projects/ionhammer/expander.cpp
delete mode 100644 src/projects/ionhammer/expander.hpp
create mode 100644 src/projects/ionhammer/gamma_poisson_model.cpp
create mode 100644 src/projects/ionhammer/gamma_poisson_model.hpp
delete mode 100644 src/projects/ionhammer/hamcluster.cpp
delete mode 100644 src/projects/ionhammer/hamcluster.hpp
create mode 100644 src/projects/ionhammer/hamcluster_1.cpp
create mode 100644 src/projects/ionhammer/hamcluster_1.h
create mode 100644 src/projects/ionhammer/io_read_corrector.hpp
create mode 100644 src/projects/ionhammer/kmer_evaluator.cpp
create mode 100644 src/projects/ionhammer/kmer_helpers.cpp
create mode 100644 src/projects/ionhammer/kmer_helpers.h
create mode 100644 src/projects/ionhammer/normal_quality_model.cpp
create mode 100644 src/projects/ionhammer/normal_quality_model.hpp
create mode 100644 src/projects/ionhammer/penalty_estimator.hpp
create mode 100644 src/projects/ionhammer/quality_metrics.cpp
create mode 100644 src/projects/ionhammer/quality_metrics.h
create mode 100644 src/projects/ionhammer/quality_thresholds_estimator.cpp
create mode 100644 src/projects/ionhammer/quality_thresholds_estimator.h
create mode 100644 src/projects/ionhammer/read_corrector_new.hpp
create mode 100644 src/projects/ionhammer/read_corrector_structs_new.h
create mode 100644 src/projects/ionhammer/reference.cpp
create mode 100644 src/projects/ionhammer/reference.h
create mode 100644 src/projects/ionhammer/thread_utils.h
create mode 100644 src/projects/mts/Reassembly.snake
copy src/projects/{hammer/quake_correct => mts/gzstream}/gzstream.C (98%)
copy src/projects/{hammer/quake_correct => mts/gzstream}/gzstream.h (93%)
create mode 100755 src/projects/mts/multirun.py
create mode 100644 src/projects/mts/scripts/Dataset_analysis.ipynb
create mode 100755 src/projects/mts/scripts/bhtsne.py
create mode 100755 src/projects/mts/scripts/bin_profiles.py
delete mode 100755 src/projects/mts/scripts/calc_kmers_mpl.py
delete mode 100755 src/projects/mts/scripts/canopy_launch.sh
create mode 100755 src/projects/mts/scripts/choose_bins.py
create mode 100755 src/projects/mts/scripts/clusters2csv.py
create mode 100755 src/projects/mts/scripts/contig_name_filter.py
create mode 100755 src/projects/mts/scripts/convert_output.py
create mode 100755 src/projects/mts/scripts/cut_fasta.py
create mode 100755 src/projects/mts/scripts/filter_bin.py
delete mode 100755 src/projects/mts/scripts/make_points_matrix.py
delete mode 100755 src/projects/mts/scripts/parse_output.py
delete mode 100755 src/projects/mts/scripts/ref_stats.sh
create mode 100755 src/projects/mts/scripts/run_tsne.py
create mode 100755 src/projects/mts/scripts/validate.pl
copy src/projects/spades/{series_analysis.hpp => series_analysis.cpp} (50%)
copy src/{projects/mts/scripts => spades_pipeline/common}/__init__.py (100%)
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