[med-svn] [spades] 01/02: Merge tag 'debian/3.9.0+dfsg-1' into debian/jessie-backports
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 commit to branch debian/jessie-backports
in repository spades.
commit fc803c0dcb8896697a4a8fda472acff4cb24ae97
Merge: c0f09ab b02e2ba
Author: Afif Elghraoui <afif at ghraoui.name>
Date: Sat Jul 30 19:32:23 2016 -0700
Merge tag 'debian/3.9.0+dfsg-1' into debian/jessie-backports
spades Debian release 3.9.0+dfsg-1
Conflicts:
debian/man_src/spades.1.adoc
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 +
configs/debruijn/simplification.info.template | 0
debian/changelog | 14 +
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 +-
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 +
224 files changed, 5375 insertions(+), 26696 deletions(-)
diff --cc debian/changelog
index 0bcf8e4,d214f7a..b568db4
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,10 -1,17 +1,24 @@@
+ spades (3.9.0+dfsg-1) unstable; urgency=medium
+
+ * New upstream release.
+ * Add copyright entry for cxxopts.
+ * Add rnaSPAdes manpage, wrappers, tests.
+
+ -- Sascha Steinbiss <satta at debian.org> Sun, 24 Jul 2016 13:12:31 +0000
+
+ spades (3.8.2+dfsg2-1) unstable; urgency=medium
+
+ * Make sure bundled headers are not used by cleaning orig tarball.
+
+ -- Sascha Steinbiss <satta at debian.org> Tue, 19 Jul 2016 20:57:51 +0000
+
+spades (3.8.2+dfsg-1~bpo8+1) UNRELEASED; urgency=medium
+
+ * Rebuild for jessie-backports.
+ * Switch manpage building back to asciidoctor.
+
+ -- Afif Elghraoui <afif at debian.org> Sun, 17 Jul 2016 20:43:22 -0700
+
spades (3.8.2+dfsg-1) unstable; urgency=medium
* New upstream release.
--
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