[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%)

-- 
Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/spades.git



More information about the debian-med-commit mailing list