[med-svn] [spades] branch upstream updated (edff796 -> 4fe3eea)
Sascha Steinbiss
satta at debian.org
Sun Jul 24 13:35:42 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch upstream
in repository spades.
from edff796 Imported Upstream version 3.8.2+dfsg2
new 4fe3eea Imported Upstream version 3.9.0+dfsg
The 1 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:
VERSION | 3 +-
changelog.html | 8 +
configs/debruijn/config.info | 12 +-
configs/debruijn/detail_info_printer.info | 2 +
configs/debruijn/log.properties | 2 +
configs/debruijn/pe_params.info | 12 +-
configs/debruijn/rna_mode.info | 50 +-
configs/debruijn/simplification.info | 13 +
.../debruijn/simplification.info.template | 0
ext/include/cxxopts/cxxopts.hpp | 1368 ++++++++++++++++++++
ext/include/llvm/Support/MathExtras.h | 1 -
ext/src/bamtools/api/internal/io/pbgzf/bgzf.c | 4 +-
ext/src/bamtools/api/internal/io/pbgzf/bgzf.h | 4 +-
ext/src/llvm/CMakeLists.txt | 3 -
manual.html | 80 +-
metaspades.py | 57 +-
plasmidspades.py | 57 +-
metaspades.py => rnaspades.py | 57 +-
rnaspades_manual.html | 84 ++
spades.py | 57 +-
src/CMakeLists.txt | 9 +-
src/cmake/pack.cmake | 6 +-
.../algorithms/genome_consistance_checker.cpp | 2 +-
src/modules/algorithms/graph_construction.hpp | 9 +-
src/modules/algorithms/mismatch_shall_not_pass.hpp | 15 +-
.../algorithms/path_extend/extension_chooser.hpp | 60 +-
.../algorithms/path_extend/overlap_analysis.hpp | 14 +-
.../algorithms/path_extend/path_extend_launch.hpp | 862 +++++++-----
.../algorithms/path_extend/path_extender.hpp | 223 +++-
src/modules/algorithms/path_extend/path_filter.hpp | 50 +-
.../algorithms/path_extend/pe_config_struct.cpp | 67 +-
.../algorithms/path_extend/pe_config_struct.hpp | 365 +++---
src/modules/algorithms/path_extend/pe_io.hpp | 13 +-
src/modules/algorithms/path_extend/pe_resolver.hpp | 7 +-
.../scaffolder2015/extension_chooser2015.hpp | 22 +-
.../algorithms/path_extend/utils/CMakeLists.txt | 13 -
.../algorithms/path_extend/utils/find_aligns.py | 67 -
.../path_extend/utils/find_single_threshold.py | 101 --
.../path_extend/utils/paired_info_checker.cpp | 204 ---
.../path_extend/utils/run_all_parametrs.py | 47 -
.../erroneous_connection_remover.hpp | 123 ++
.../algorithms/simplification/tip_clipper.hpp | 12 +-
src/modules/assembly_graph/CMakeLists.txt | 2 +-
.../assembly_graph/graph_alignment/edge_index.hpp | 41 +-
.../graph_alignment/edge_index_refiller.cpp | 33 +
.../graph_alignment/edge_index_refiller.hpp | 20 +
.../assembly_graph/graph_alignment/kmer_mapper.hpp | 5 +
.../graph_alignment/pacbio/pac_index.hpp | 82 +-
.../graph_alignment/pacbio/pacbio_gap_closer.hpp | 20 +-
.../pacbio/pacbio_read_structures.hpp | 12 +-
.../graph_alignment/sequence_mapper.hpp | 69 +-
.../graph_alignment/sequence_mapper_notifier.hpp | 3 +
.../graph_alignment/short_read_mapper.hpp | 2 +-
.../graph_support/basic_edge_conditions.hpp | 1 +
.../assembly_graph/graph_support/contig_output.hpp | 22 +-
.../graph_support/genomic_quality.hpp | 6 +-
.../handlers/edges_position_handler.hpp | 6 +
src/modules/assembly_graph/paths/mapping_path.hpp | 5 +
src/modules/assembly_graph/stats/picture_dump.hpp | 21 +
.../debruijn_graph/debruijn_graph_constructor.hpp | 7 -
.../debruijn_graph/early_simplification.hpp | 81 +-
.../indices/edge_index_builders.hpp | 33 +-
.../data_structures/indices/edge_info_updater.hpp | 1 +
.../data_structures/indices/edge_multi_index.hpp | 8 +-
.../indices/edge_position_index.hpp | 29 +-
.../data_structures/indices/key_with_hash.hpp | 38 +-
.../indices/kmer_extension_index.hpp | 108 +-
.../indices/kmer_extension_index_builder.hpp | 106 ++
.../data_structures/indices/kmer_splitters.hpp | 249 +---
.../data_structures/indices/perfect_hash_map.hpp | 112 +-
.../indices/perfect_hash_map_builder.hpp | 102 ++
.../data_structures/mph_index/kmer_index.hpp | 403 +-----
.../{kmer_index.hpp => kmer_index_builder.hpp} | 394 ++----
.../mph_index/kmer_index_traits.hpp | 87 ++
src/modules/data_structures/mph_index/mphf.hpp | 2 +-
src/modules/data_structures/sequence/rtseq.hpp | 16 +-
src/modules/data_structures/sequence/sequence.hpp | 11 +
.../data_structures/sequence/simple_seq.hpp | 5 +-
src/modules/io/dataset_support/read_converter.hpp | 403 +++---
.../io/reads_io/modifying_reader_wrapper.hpp | 1 +
src/modules/io/reads_io/mpmc_bounded.hpp | 27 +-
src/modules/io/reads_io/paired_readers.hpp | 1 +
src/modules/io/reads_io/read_processor.hpp | 62 +-
src/modules/io/reads_io/splitting_wrapper.hpp | 1 +
src/modules/math/kmer_coverage_model.cpp | 4 +-
src/modules/paired_info/pair_info_improver.hpp | 6 +-
src/modules/pipeline/config_struct.cpp | 47 +-
src/modules/pipeline/config_struct.hpp | 46 +-
src/modules/pipeline/genomic_info_filler.cpp | 2 +-
src/modules/pipeline/graph_pack.hpp | 8 +-
src/modules/pipeline/library.hpp | 5 +-
src/modules/stages/construction.cpp | 9 +-
src/modules/stages/simplification.cpp | 87 +-
.../graph_simplification.hpp | 258 ++--
.../simplification_settings.hpp | 11 +-
src/modules/visualization/position_filler.hpp | 4 +-
src/modules/visualization/visualization_utils.hpp | 12 +-
src/projects/CMakeLists.txt | 11 +-
src/projects/cap/cap_kmer_index.hpp | 11 -
src/projects/cap/mosaic.hpp | 2 +-
src/projects/hammer/expander.cpp | 8 +-
src/projects/hammer/expander.hpp | 3 +-
src/projects/hammer/kmer_cluster.cpp | 2 +
src/projects/hammer/kmer_data.cpp | 495 +++----
src/projects/ionhammer/hamcluster.hpp | 1 -
src/projects/ionhammer/kmer_data.cpp | 121 +-
src/projects/ionhammer/read_corrector.hpp | 56 +-
src/projects/mph_test/CMakeLists.txt | 15 +
src/projects/mph_test/main.cpp | 184 +++
.../online_vis/debruijn_online_visualizer.hpp | 2 +-
.../drawing_commands/draw_contig_command.hpp | 12 +-
.../drawing_commands/draw_missasemblies.hpp | 25 +-
.../drawing_commands/draw_poorly_assembled.hpp | 135 +-
.../drawing_commands/drawing_command.hpp | 7 +-
.../position_commands/fill_position_command.hpp | 11 +-
src/projects/online_vis/processing_commands.hpp | 2 +-
src/projects/online_vis/vis_logger.hpp | 6 +-
.../scaffold_correction/scaffold_correction.hpp | 1 +
src/projects/spades/chromosome_removal.cpp | 2 +-
src/projects/spades/distance_estimation.cpp | 5 +-
src/projects/spades/gap_closer.cpp | 7 +-
src/projects/spades/main.cpp | 1 +
src/projects/spades/mismatch_correction.cpp | 8 +-
src/projects/spades/pacbio_aligning.cpp | 8 +-
src/projects/spades/pair_info_count.cpp | 12 +-
src/projects/spades/repeat_resolving.cpp | 35 +-
src/projects/truseq_analysis/analysis_pipeline.cpp | 1 +
src/spades_pipeline/options_storage.py | 84 +-
src/spades_pipeline/spades_logic.py | 54 +-
src/utils/adt/bf.hpp | 174 +++
src/utils/adt/hll.hpp | 69 +
131 files changed, 5295 insertions(+), 3576 deletions(-)
copy ext/src/samtools/examples/ex1.glf => configs/debruijn/simplification.info.template (100%)
create mode 100644 ext/include/cxxopts/cxxopts.hpp
copy metaspades.py => rnaspades.py (93%)
create mode 100644 rnaspades_manual.html
delete mode 100644 src/modules/algorithms/path_extend/utils/CMakeLists.txt
delete mode 100644 src/modules/algorithms/path_extend/utils/find_aligns.py
delete mode 100644 src/modules/algorithms/path_extend/utils/find_single_threshold.py
delete mode 100644 src/modules/algorithms/path_extend/utils/paired_info_checker.cpp
delete mode 100644 src/modules/algorithms/path_extend/utils/run_all_parametrs.py
create mode 100644 src/modules/assembly_graph/graph_alignment/edge_index_refiller.cpp
create mode 100644 src/modules/assembly_graph/graph_alignment/edge_index_refiller.hpp
create mode 100644 src/modules/data_structures/indices/kmer_extension_index_builder.hpp
create mode 100644 src/modules/data_structures/indices/perfect_hash_map_builder.hpp
copy src/modules/data_structures/mph_index/{kmer_index.hpp => kmer_index_builder.hpp} (53%)
create mode 100644 src/modules/data_structures/mph_index/kmer_index_traits.hpp
create mode 100644 src/projects/mph_test/CMakeLists.txt
create mode 100644 src/projects/mph_test/main.cpp
create mode 100644 src/utils/adt/bf.hpp
create mode 100644 src/utils/adt/hll.hpp
--
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