[med-svn] [spades] branch debian/jessie-backports updated (c0f09ab -> 117634e)
Afif Elghraoui
afif at moszumanska.debian.org
Mon Aug 22 05:25:54 UTC 2016
This is an automated email from the git hooks/post-receive script.
afif pushed a change to branch debian/jessie-backports
in repository spades.
from c0f09ab Prepare backports revision
adds 2d1ec75 use repacked tarball
adds edff796 Imported Upstream version 3.8.2+dfsg2
adds 7356743 Merge tag 'upstream/3.8.2+dfsg2'
adds 56f008a do not use bundled headers
adds 4fe3eea Imported Upstream version 3.9.0+dfsg
adds 4075290 Merge tag 'upstream/3.9.0+dfsg'
adds 109110e new upstream version
adds 500cacf add rnaSPAdes
adds b76ca71 add manpage link
adds b02e2ba dch -r
new fc803c0 Merge tag 'debian/3.9.0+dfsg-1' into debian/jessie-backports
new 117634e releasing package spades version 3.9.0+dfsg-1~bpo8+1
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:
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 | 18 +-
debian/copyright | 15 +-
debian/links | 3 +
debian/man_src/{spades.1.adoc => rnaspades.1.adoc} | 52 +-
debian/man_src/spades.1.adoc | 11 +-
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 | 35 +-
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/htrie/ahtable.h | 115 -
ext/include/htrie/common.h | 22 -
ext/include/htrie/hat-trie.h | 74 -
ext/include/llvm/Support/MathExtras.h | 1 -
ext/include/nlopt/auglag.h | 50 -
ext/include/nlopt/bobyqa.h | 13 -
ext/include/nlopt/cdirect.h | 80 -
ext/include/nlopt/cobyla.h | 62 -
ext/include/nlopt/crs.h | 47 -
ext/include/nlopt/esch.h | 49 -
ext/include/nlopt/isres.h | 48 -
ext/include/nlopt/mlsl.h | 48 -
ext/include/nlopt/mma.h | 61 -
ext/include/nlopt/neldermead.h | 61 -
ext/include/nlopt/newuoa.h | 14 -
ext/include/nlopt/nlopt-internal.h | 95 -
ext/include/nlopt/nlopt-util.h | 124 -
ext/include/nlopt/nlopt.h | 379 ---
ext/include/nlopt/nlopt.hpp | 596 ----
ext/include/nlopt/praxis.h | 22 -
ext/include/nlopt/redblack.h | 77 -
ext/include/ssw/ssw.h | 188 --
ext/include/ssw/ssw_cpp.h | 215 --
ext/src/bamtools/api/internal/io/pbgzf/bgzf.c | 4 +-
ext/src/bamtools/api/internal/io/pbgzf/bgzf.h | 4 +-
ext/src/htrie/CMakeLists.txt | 11 -
ext/src/htrie/ahtable.c | 564 ----
ext/src/htrie/hat-trie.c | 711 -----
ext/src/htrie/misc.c | 46 -
ext/src/htrie/misc.h | 22 -
ext/src/htrie/murmurhash3.c | 77 -
ext/src/htrie/murmurhash3.h | 12 -
ext/src/llvm/CMakeLists.txt | 3 -
ext/src/nlopt/AUTHORS | 6 -
ext/src/nlopt/CMakeLists.txt | 34 -
ext/src/nlopt/COPYING | 20 -
ext/src/nlopt/api/deprecated.c | 171 -
ext/src/nlopt/api/general.c | 134 -
ext/src/nlopt/api/optimize.c | 767 -----
ext/src/nlopt/api/options.c | 753 -----
ext/src/nlopt/auglag/README | 25 -
ext/src/nlopt/auglag/auglag.c | 289 --
ext/src/nlopt/bobyqa/COPYRIGHT | 23 -
ext/src/nlopt/bobyqa/README | 20 -
ext/src/nlopt/bobyqa/README.orig | 60 -
ext/src/nlopt/bobyqa/bobyqa.c | 3269 --------------------
ext/src/nlopt/cdirect/README | 26 -
ext/src/nlopt/cdirect/cdirect.c | 600 ----
ext/src/nlopt/cdirect/hybrid.c | 317 --
ext/src/nlopt/cobyla/COPYRIGHT | 22 -
ext/src/nlopt/cobyla/README | 42 -
ext/src/nlopt/cobyla/README.orig | 74 -
ext/src/nlopt/cobyla/cobyla.c | 1847 -----------
ext/src/nlopt/crs/README | 19 -
ext/src/nlopt/crs/crs.c | 270 --
ext/src/nlopt/esch/COPYRIGHT | 22 -
ext/src/nlopt/esch/README | 27 -
ext/src/nlopt/esch/esch.c | 259 --
ext/src/nlopt/isres/README | 23 -
ext/src/nlopt/isres/isres.c | 283 --
ext/src/nlopt/mlsl/README | 22 -
ext/src/nlopt/mlsl/mlsl.c | 435 ---
ext/src/nlopt/mma/README | 32 -
ext/src/nlopt/mma/ccsa_quadratic.c | 550 ----
ext/src/nlopt/mma/mma.c | 398 ---
ext/src/nlopt/neldermead/README | 107 -
ext/src/nlopt/neldermead/nldrmd.c | 306 --
ext/src/nlopt/neldermead/sbplx.c | 239 --
ext/src/nlopt/newuoa/COPYRIGHT | 23 -
ext/src/nlopt/newuoa/README | 29 -
ext/src/nlopt/newuoa/README.orig | 40 -
ext/src/nlopt/newuoa/newuoa.c | 2560 ---------------
ext/src/nlopt/praxis/README | 15 -
ext/src/nlopt/praxis/praxis.c | 1366 --------
ext/src/nlopt/util/mt19937ar.c | 241 --
ext/src/nlopt/util/qsort_r.c | 110 -
ext/src/nlopt/util/redblack.c | 430 ---
ext/src/nlopt/util/rescale.c | 82 -
ext/src/nlopt/util/soboldata.h | 880 ------
ext/src/nlopt/util/sobolseq.c | 287 --
ext/src/nlopt/util/stop.c | 134 -
ext/src/nlopt/util/timer.c | 93 -
ext/src/ssw/CMakeLists.txt | 12 -
ext/src/ssw/ssw.c | 903 ------
ext/src/ssw/ssw_cpp.cpp | 477 ---
manual.html | 80 +-
metaspades.py | 57 +-
plasmidspades.py | 57 +-
plasmidspades.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 +
224 files changed, 5377 insertions(+), 26698 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
delete mode 100644 ext/include/htrie/ahtable.h
delete mode 100644 ext/include/htrie/common.h
delete mode 100644 ext/include/htrie/hat-trie.h
delete mode 100644 ext/include/nlopt/auglag.h
delete mode 100644 ext/include/nlopt/bobyqa.h
delete mode 100644 ext/include/nlopt/cdirect.h
delete mode 100644 ext/include/nlopt/cobyla.h
delete mode 100644 ext/include/nlopt/crs.h
delete mode 100644 ext/include/nlopt/esch.h
delete mode 100644 ext/include/nlopt/isres.h
delete mode 100644 ext/include/nlopt/mlsl.h
delete mode 100644 ext/include/nlopt/mma.h
delete mode 100644 ext/include/nlopt/neldermead.h
delete mode 100644 ext/include/nlopt/newuoa.h
delete mode 100644 ext/include/nlopt/nlopt-internal.h
delete mode 100644 ext/include/nlopt/nlopt-util.h
delete mode 100644 ext/include/nlopt/nlopt.h
delete mode 100644 ext/include/nlopt/nlopt.hpp
delete mode 100644 ext/include/nlopt/praxis.h
delete mode 100644 ext/include/nlopt/redblack.h
delete mode 100755 ext/include/ssw/ssw.h
delete mode 100644 ext/include/ssw/ssw_cpp.h
delete mode 100644 ext/src/htrie/CMakeLists.txt
delete mode 100644 ext/src/htrie/ahtable.c
delete mode 100644 ext/src/htrie/hat-trie.c
delete mode 100644 ext/src/htrie/misc.c
delete mode 100644 ext/src/htrie/misc.h
delete mode 100644 ext/src/htrie/murmurhash3.c
delete mode 100644 ext/src/htrie/murmurhash3.h
delete mode 100644 ext/src/nlopt/AUTHORS
delete mode 100644 ext/src/nlopt/CMakeLists.txt
delete mode 100644 ext/src/nlopt/COPYING
delete mode 100644 ext/src/nlopt/api/deprecated.c
delete mode 100644 ext/src/nlopt/api/general.c
delete mode 100644 ext/src/nlopt/api/optimize.c
delete mode 100644 ext/src/nlopt/api/options.c
delete mode 100644 ext/src/nlopt/auglag/README
delete mode 100644 ext/src/nlopt/auglag/auglag.c
delete mode 100644 ext/src/nlopt/bobyqa/COPYRIGHT
delete mode 100644 ext/src/nlopt/bobyqa/README
delete mode 100644 ext/src/nlopt/bobyqa/README.orig
delete mode 100644 ext/src/nlopt/bobyqa/bobyqa.c
delete mode 100644 ext/src/nlopt/cdirect/README
delete mode 100644 ext/src/nlopt/cdirect/cdirect.c
delete mode 100644 ext/src/nlopt/cdirect/hybrid.c
delete mode 100644 ext/src/nlopt/cobyla/COPYRIGHT
delete mode 100644 ext/src/nlopt/cobyla/README
delete mode 100644 ext/src/nlopt/cobyla/README.orig
delete mode 100644 ext/src/nlopt/cobyla/cobyla.c
delete mode 100644 ext/src/nlopt/crs/README
delete mode 100644 ext/src/nlopt/crs/crs.c
delete mode 100644 ext/src/nlopt/esch/COPYRIGHT
delete mode 100644 ext/src/nlopt/esch/README
delete mode 100644 ext/src/nlopt/esch/esch.c
delete mode 100644 ext/src/nlopt/isres/README
delete mode 100644 ext/src/nlopt/isres/isres.c
delete mode 100644 ext/src/nlopt/mlsl/README
delete mode 100644 ext/src/nlopt/mlsl/mlsl.c
delete mode 100644 ext/src/nlopt/mma/README
delete mode 100644 ext/src/nlopt/mma/ccsa_quadratic.c
delete mode 100644 ext/src/nlopt/mma/mma.c
delete mode 100644 ext/src/nlopt/neldermead/README
delete mode 100644 ext/src/nlopt/neldermead/nldrmd.c
delete mode 100644 ext/src/nlopt/neldermead/sbplx.c
delete mode 100644 ext/src/nlopt/newuoa/COPYRIGHT
delete mode 100644 ext/src/nlopt/newuoa/README
delete mode 100644 ext/src/nlopt/newuoa/README.orig
delete mode 100644 ext/src/nlopt/newuoa/newuoa.c
delete mode 100644 ext/src/nlopt/praxis/README
delete mode 100644 ext/src/nlopt/praxis/praxis.c
delete mode 100644 ext/src/nlopt/util/mt19937ar.c
delete mode 100644 ext/src/nlopt/util/qsort_r.c
delete mode 100644 ext/src/nlopt/util/redblack.c
delete mode 100644 ext/src/nlopt/util/rescale.c
delete mode 100644 ext/src/nlopt/util/soboldata.h
delete mode 100644 ext/src/nlopt/util/sobolseq.c
delete mode 100644 ext/src/nlopt/util/stop.c
delete mode 100644 ext/src/nlopt/util/timer.c
delete mode 100644 ext/src/ssw/CMakeLists.txt
delete mode 100755 ext/src/ssw/ssw.c
delete mode 100644 ext/src/ssw/ssw_cpp.cpp
copy plasmidspades.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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