[med-svn] [spades] branch master updated (56f008a -> b02e2ba)
Sascha Steinbiss
satta at debian.org
Sun Jul 24 13:35:41 UTC 2016
This is an automated email from the git hooks/post-receive script.
satta pushed a change to branch master
in repository spades.
from 56f008a do not use bundled headers
new 4fe3eea Imported Upstream version 3.9.0+dfsg
new 4075290 Merge tag 'upstream/3.9.0+dfsg'
new 109110e new upstream version
new 500cacf add rnaSPAdes
new b76ca71 add manpage link
new b02e2ba dch -r
The 6 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
debian/changelog | 8 +
debian/copyright | 4 +
debian/links | 3 +
debian/man_src/{spades.1.adoc => rnaspades.1.adoc} | 52 +-
debian/man_src/spades.1.adoc | 5 +-
debian/patches/0003_accept-system-bwa.patch | 2 +-
debian/patches/0103_use-debian-packaged-bwa.patch | 4 +-
debian/patches/0111_use_full_config_dirs.patch | 4 +-
debian/patches/0114_use_debian_provided_libs.patch | 2 +-
debian/patches/0116_stable_link_order.patch | 2 +-
debian/rules | 1 +
debian/tests/run-upstreams-tests | 1 +
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 +
143 files changed, 5327 insertions(+), 3632 deletions(-)
copy ext/src/samtools/examples/ex1.glf => configs/debruijn/simplification.info.template (100%)
copy debian/man_src/{spades.1.adoc => rnaspades.1.adoc} (55%)
create mode 100644 ext/include/cxxopts/cxxopts.hpp
copy metaspades.py => rnaspades.py (93%)
create mode 100644 rnaspades_manual.html
delete mode 100644 src/modules/algorithms/path_extend/utils/CMakeLists.txt
delete mode 100644 src/modules/algorithms/path_extend/utils/find_aligns.py
delete mode 100644 src/modules/algorithms/path_extend/utils/find_single_threshold.py
delete mode 100644 src/modules/algorithms/path_extend/utils/paired_info_checker.cpp
delete mode 100644 src/modules/algorithms/path_extend/utils/run_all_parametrs.py
create mode 100644 src/modules/assembly_graph/graph_alignment/edge_index_refiller.cpp
create mode 100644 src/modules/assembly_graph/graph_alignment/edge_index_refiller.hpp
create mode 100644 src/modules/data_structures/indices/kmer_extension_index_builder.hpp
create mode 100644 src/modules/data_structures/indices/perfect_hash_map_builder.hpp
copy src/modules/data_structures/mph_index/{kmer_index.hpp => kmer_index_builder.hpp} (53%)
create mode 100644 src/modules/data_structures/mph_index/kmer_index_traits.hpp
create mode 100644 src/projects/mph_test/CMakeLists.txt
create mode 100644 src/projects/mph_test/main.cpp
create mode 100644 src/utils/adt/bf.hpp
create mode 100644 src/utils/adt/hll.hpp
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