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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 | 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.../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 +- 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.../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 _______________________________________________ debian-med-commit mailing list debian-med-commit@lists.alioth.debian.org http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit