[med-svn] [spades] 01/04: Merge branch 'master' into ubuntu/trusty-backports
Sascha Steinbiss
sascha at steinbiss.name
Tue Mar 22 10:43:54 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a commit to branch ubuntu/trusty-backports
in repository spades.
commit dd546f7aef0dc84748e4b887ca6bda00d811f4a1
Merge: c2bbc53 3bdfebf
Author: Sascha Steinbiss <sascha at steinbiss.name>
Date: Tue Mar 22 01:21:35 2016 +0000
Merge branch 'master' into ubuntu/trusty-backports
LICENSE | 16 +-
README | 14 +-
VERSION | 2 +-
changelog.html | 18 +-
configs/corrector/corrector.info | 7 +
.../debruijn/{config.info.template => config.info} | 23 +-
configs/debruijn/config.info.template | 23 +-
configs/debruijn/construction.info | 23 +
configs/debruijn/coverage_based_rr.info.template | 13 -
configs/debruijn/detail_info_printer.info | 43 +
configs/debruijn/detail_info_printer.info.template | 47 +-
configs/debruijn/distance_estimation.info | 91 +
.../{log.properties.template => log.properties} | 8 +
configs/debruijn/log.properties.template | 8 +
configs/debruijn/path_extend/pe_params.info | 186 ++
.../debruijn/path_extend/pe_params.info.template | 257 +--
configs/debruijn/simplification.info | 561 +++++
configs/debruijn/simplification.info.template | 647 +++---
configs/debruijn/tsa.info | 5 +
configs/dipspades/config.info | 64 +
.../log.properties} | 26 +-
.../hammer/{config.info.template => config.info} | 4 +-
configs/hammer/config.info.template | 4 +-
configs/ionhammer/ionhammer.cfg | 12 +
debian/changelog | 37 +
debian/control | 10 +-
debian/copyright | 58 +-
debian/gbp.conf | 2 +
.../man_src/{dipspades.1.ronn => dipspades.1.adoc} | 101 +-
debian/man_src/{spades.1.ronn => spades.1.adoc} | 103 +-
.../man_src/{truspades.1.ronn => truspades.1.adoc} | 27 +-
.../0001_use_debian_packaged_python-yaml.patch | 76 -
debian/patches/0003_accept-system-bwa.patch | 12 +-
.../0101_cmake_ignore_removed_python-yaml.patch | 6 +-
.../0102_cmake_ignore_removed_python-joblib.patch | 4 +-
debian/patches/0103_use-debian-packaged-bwa.patch | 4 +-
debian/patches/0110_build_single_thread.patch | 4 +-
debian/patches/0111_use_full_config_dirs.patch | 18 +-
debian/patches/0112_spelling.patch | 18 +-
debian/patches/0113_adjust_paths.patch | 43 +-
debian/patches/0114_use_debian_provided_libs.patch | 79 +
.../0120_dont_rename_jemalloc_functionnames.patch | 10 +
debian/patches/series | 2 +-
debian/rules | 10 +-
debian/source.lintian-overrides | 2 +
dipspades.py | 14 +-
dipspades_manual.html | 6 +
ext/include/city/city.h | 109 +
ext/include/city/citycrc.h | 43 +
ext/include/jemalloc/internal/arena.h | 975 --------
ext/include/jemalloc/internal/atomic.h | 304 ---
ext/include/jemalloc/internal/base.h | 26 -
ext/include/jemalloc/internal/bitmap.h | 184 --
ext/include/jemalloc/internal/chunk.h | 63 -
ext/include/jemalloc/internal/chunk_dss.h | 38 -
ext/include/jemalloc/internal/chunk_mmap.h | 22 -
ext/include/jemalloc/internal/ckh.h | 90 -
ext/include/jemalloc/internal/ctl.h | 117 -
ext/include/jemalloc/internal/extent.h | 46 -
ext/include/jemalloc/internal/hash.h | 70 -
ext/include/jemalloc/internal/huge.h | 40 -
ext/include/jemalloc/internal/jemalloc_internal.h | 1010 ---------
ext/include/jemalloc/internal/mb.h | 115 -
ext/include/jemalloc/internal/mutex.h | 99 -
ext/include/jemalloc/internal/private_namespace.h | 367 ---
ext/include/jemalloc/internal/prng.h | 60 -
ext/include/jemalloc/internal/prof.h | 581 -----
ext/include/jemalloc/internal/ql.h | 83 -
ext/include/jemalloc/internal/qr.h | 67 -
ext/include/jemalloc/internal/quarantine.h | 24 -
ext/include/jemalloc/internal/rb.h | 973 --------
ext/include/jemalloc/internal/rtree.h | 164 --
ext/include/jemalloc/internal/size_classes.h | 721 ------
ext/include/jemalloc/internal/size_classes.sh | 122 -
ext/include/jemalloc/internal/stats.h | 186 --
ext/include/jemalloc/internal/tcache.h | 440 ----
ext/include/jemalloc/internal/tsd.h | 397 ----
ext/include/jemalloc/internal/util.h | 160 --
ext/include/jemalloc/jemalloc.h.in | 157 --
ext/include/jemalloc/jemalloc_defs.h.in | 264 ---
ext/include/llvm/AlignOf.h | 189 ++
ext/include/llvm/PointerEmbeddedInt.h | 87 +
ext/include/llvm/PointerIntPair.h | 192 ++
ext/include/llvm/PointerLikeTypeTraits.h | 92 +
ext/include/llvm/PointerSumType.h | 176 ++
ext/src/CMakeLists.txt | 3 +-
ext/src/ConsensusCore/Version.cpp | 2 +-
{src/mph_index => ext/src/cityhash}/CMakeLists.txt | 8 +-
ext/src/cityhash/city.cc | 639 ++++++
ext/src/jemalloc/CMakeLists.txt | 213 --
ext/src/jemalloc/COPYING | 27 -
ext/src/jemalloc/arena.c | 2376 --------------------
ext/src/jemalloc/atomic.c | 2 -
ext/src/jemalloc/base.c | 139 --
ext/src/jemalloc/bitmap.c | 90 -
ext/src/jemalloc/chunk.c | 381 ----
ext/src/jemalloc/chunk_dss.c | 197 --
ext/src/jemalloc/chunk_mmap.c | 210 --
ext/src/jemalloc/ckh.c | 609 -----
ext/src/jemalloc/cmake/CheckPageSize.c.in | 18 -
ext/src/jemalloc/ctl.c | 1674 --------------
ext/src/jemalloc/extent.c | 39 -
ext/src/jemalloc/hash.c | 2 -
ext/src/jemalloc/huge.c | 313 ---
ext/src/jemalloc/intercept.inl | 67 -
ext/src/jemalloc/jemalloc.c | 1848 ---------------
ext/src/jemalloc/mb.c | 2 -
ext/src/jemalloc/mutex.c | 149 --
ext/src/jemalloc/prof.c | 1315 -----------
ext/src/jemalloc/quarantine.c | 210 --
ext/src/jemalloc/rtree.c | 67 -
ext/src/jemalloc/stats.c | 551 -----
ext/src/jemalloc/tcache.c | 474 ----
ext/src/jemalloc/tsd.c | 107 -
ext/src/jemalloc/util.c | 641 ------
ext/src/jemalloc/zone.c | 257 ---
ext/src/ssw/ssw.c | 349 +--
ext/src/ssw/ssw_cpp.cpp | 258 ++-
manual.html | 151 +-
spades.py | 21 +-
spades_init.py | 2 +-
src/CMakeLists.txt | 7 +-
src/cmake/pack.cmake | 6 +-
src/corrector/CMakeLists.txt | 14 +-
src/corrector/contig_processor.cpp | 132 +-
src/corrector/contig_processor.hpp | 14 +-
src/corrector/dataset_processor.cpp | 50 +-
src/corrector/dataset_processor.hpp | 3 +-
src/corrector/interesting_pos_processor.hpp | 2 +-
src/corrector/main.cpp | 4 +-
src/corrector/read.cpp | 164 --
src/debruijn/CMakeLists.txt | 15 +-
src/debruijn/bwa_pair_info_filler.cpp | 407 ++++
src/debruijn/bwa_pair_info_filler.hpp | 254 +++
src/debruijn/config_struct.cpp | 169 +-
src/debruijn/config_struct.hpp | 66 +-
src/debruijn/construction.cpp | 4 +-
src/debruijn/dataset_readers.hpp | 12 +-
src/debruijn/debruijn_data.hpp | 15 +-
src/debruijn/debruijn_stats.cpp | 1050 ++++-----
src/debruijn/detail_coverage.hpp | 3 +
src/debruijn/distance_estimation.cpp | 14 +-
src/debruijn/early_simplification.hpp | 52 +-
src/debruijn/gap_closer.cpp | 58 +-
src/debruijn/genome_consistance_checker.cpp | 236 ++
src/debruijn/genome_consistance_checker.hpp | 126 +-
src/debruijn/genome_storage.cpp | 45 +
src/debruijn/genome_storage.hpp | 33 +
src/debruijn/genomic_info_filler.cpp | 6 +-
src/debruijn/genomic_quality.hpp | 5 +
src/debruijn/graph_pack.hpp | 19 +-
src/debruijn/graph_simplification.hpp | 1000 --------
src/debruijn/graphio.hpp | 75 +-
src/debruijn/indices/edge_multi_index.hpp | 1 +
src/debruijn/indices/kmer_extension_index.hpp | 1 -
src/debruijn/indices/kmer_splitters.hpp | 8 +-
src/debruijn/indices/perfect_hash_map.hpp | 6 +
src/debruijn/is_counter.hpp | 153 +-
src/debruijn/kmer_coverage_model.cpp | 2 +-
src/debruijn/launch.hpp | 36 +-
src/debruijn/long_read_mapper.hpp | 67 +-
src/debruijn/main.cpp | 1 +
src/debruijn/mismatch_correction.cpp | 7 +-
src/debruijn/overlap_analysis.hpp | 113 +
src/debruijn/pacbio/pac_index.hpp | 71 +-
src/debruijn/pacbio/pacbio_gap_closer.hpp | 50 +-
src/debruijn/pacbio_aligning.cpp | 54 +-
src/debruijn/pair_info_count.cpp | 71 +-
src/debruijn/pair_info_filler.hpp | 43 +-
src/debruijn/pair_info_improver.hpp | 210 +-
src/debruijn/paired_statistics.hpp | 4 +-
src/debruijn/path_extend/bidirectional_path.hpp | 136 +-
src/debruijn/path_extend/extension_chooser.hpp | 581 +++--
src/debruijn/path_extend/ideal_pair_info.hpp | 9 +-
src/debruijn/path_extend/loop_traverser.hpp | 10 +-
src/debruijn/path_extend/next_path_searcher.hpp | 103 +-
src/debruijn/path_extend/paired_library.hpp | 161 +-
src/debruijn/path_extend/path_extend_launch.hpp | 446 +++-
src/debruijn/path_extend/path_extender.hpp | 673 ++++--
src/debruijn/path_extend/pe_config_struct.cpp | 166 +-
src/debruijn/path_extend/pe_config_struct.hpp | 97 +-
src/debruijn/path_extend/pe_io.hpp | 109 +-
src/debruijn/path_extend/pe_resolver.hpp | 198 +-
src/debruijn/path_extend/pe_utils.hpp | 12 +-
.../scaffolder2015/connection_condition2015.cpp | 111 +
.../scaffolder2015/connection_condition2015.hpp | 69 +
.../scaffolder2015/extension_chooser2015.cpp | 81 +
.../scaffolder2015/extension_chooser2015.hpp | 49 +
.../scaffolder2015/scaff_supplementary.cpp | 66 +
.../scaffolder2015/scaff_supplementary.hpp | 75 +
.../path_extend/scaffolder2015/scaffold_graph.cpp | 275 +++
.../path_extend/scaffolder2015/scaffold_graph.hpp | 233 ++
.../scaffolder2015/scaffold_graph_constructor.cpp | 73 +
.../scaffolder2015/scaffold_graph_constructor.hpp | 101 +
.../scaffolder2015/scaffold_graph_visualizer.cpp | 71 +
.../scaffolder2015/scaffold_graph_visualizer.hpp | 73 +
src/debruijn/path_extend/split_graph_pair_info.hpp | 90 +-
src/debruijn/path_extend/weight_counter.hpp | 500 ++--
src/debruijn/path_utils.hpp | 15 +-
src/debruijn/positions.hpp | 2 +
src/debruijn/read_converter.hpp | 61 +-
src/debruijn/repeat.hpp | 371 ---
src/debruijn/repeat_resolving.cpp | 15 +-
src/debruijn/second_phase_setup.cpp | 5 +-
src/debruijn/sequence_mapper.hpp | 227 +-
src/debruijn/sequence_mapper_notifier.hpp | 37 +-
src/debruijn/simplification.cpp | 399 +++-
.../simplification/graph_simplification.hpp | 825 +++++++
.../parallel_simplification_algorithms.hpp | 351 ++-
.../simplification/simplification_settings.hpp | 212 +-
.../simplification/single_cell_simplification.hpp | 110 +
src/debruijn/split_path_constructor.hpp | 19 +-
src/debruijn/stage.hpp | 8 +-
src/debruijn/stats/debruijn_stats.hpp | 243 +-
.../contig_correctors/close_gaps_corrector.hpp | 4 +-
.../contig_correctors/overlap_searcher.hpp | 8 +-
.../contig_correctors/redundant_contig_remover.hpp | 8 +-
src/dipspades/dipspades.hpp | 14 +-
src/dipspades/dipspades_config.cpp | 2 +-
src/dipspades/dipspades_config.hpp | 2 +-
src/dipspades/main.cpp | 31 +-
.../bulge_paths_searcher.hpp | 9 +-
src/hammer/CMakeLists.txt | 2 +-
src/hammer/config_struct_hammer.cpp | 4 +-
src/hammer/config_struct_hammer.hpp | 2 +
src/hammer/expander.cpp | 14 +-
src/hammer/hamcluster.cpp | 86 +-
src/hammer/hamcluster.hpp | 9 +
src/hammer/hammer_tools.cpp | 4 +-
src/hammer/kmer_data.cpp | 265 ++-
src/hammer/main.cpp | 15 +-
src/hammer/misc/memusg | 2 +-
src/hammer/read_corrector.cpp | 45 +-
src/hammer/read_corrector.hpp | 7 +-
src/include/adt/concurrent_dsu.hpp | 314 +--
src/include/adt/flat_map.hpp | 320 +++
src/include/adt/flat_set.hpp | 230 ++
src/include/adt/function_traits.hpp | 70 +
src/include/adt/iterator_range.hpp | 13 +
src/include/adt/queue_iterator.hpp | 14 +
src/include/adt/small_pod_vector.hpp | 379 ++++
src/include/de/conj_iterator.hpp | 140 ++
src/include/de/data_divider.hpp | 2 +-
src/include/de/distance_estimation.hpp | 60 +-
src/include/de/extensive_distance_estimation.hpp | 69 +-
src/include/de/index_point.hpp | 455 ++++
src/include/de/insert_size_refiner.hpp | 97 +-
src/include/de/pair_info_filters.hpp | 161 +-
src/include/de/paired_info.hpp | 1417 ++++++------
src/include/de/paired_info_helpers.hpp | 149 ++
src/include/de/smoothing_distance_estimation.hpp | 33 +-
src/include/de/weighted_distance_estimation.hpp | 14 +-
src/include/func.hpp | 116 +-
src/include/graph_print_utils.hpp | 4 +-
src/include/io/kmer_iterator.hpp | 54 +
src/include/io/library.hpp | 48 +-
src/include/io/mmapped_reader.hpp | 68 +-
src/include/io/paired_read.hpp | 100 +-
src/include/io/read.hpp | 7 +-
src/{corrector => include/io/sam}/read.hpp | 101 +-
src/{corrector => include/io/sam}/sam_reader.hpp | 5 +-
src/include/io/single_read.hpp | 171 +-
src/include/logger/logger.hpp | 1 +
src/include/mph_index/MurmurHash3.h | 38 -
src/include/mph_index/base_hash.hpp | 67 +-
src/include/mph_index/kmer_index.hpp | 10 +-
src/include/omni/action_handlers.hpp | 4 +-
src/include/omni/basic_edge_conditions.hpp | 42 +-
src/include/omni/bulge_remover.hpp | 784 +++++--
src/include/omni/complex_bulge_remover.hpp | 13 +-
src/include/omni/complex_tip_clipper.hpp | 8 +-
src/include/omni/coverage.hpp | 21 +-
.../omni/dijkstra_tools/dijkstra_algorithm.hpp | 354 +--
.../omni/dijkstra_tools/dijkstra_helper.hpp | 50 +-
.../omni/dijkstra_tools/dijkstra_settings.hpp | 19 +-
.../omni/dijkstra_tools/vertex_process_checker.hpp | 55 +-
src/include/omni/edges_position_handler.hpp | 4 +
src/include/omni/erroneous_connection_remover.hpp | 73 +-
src/include/omni/graph_component.hpp | 6 +-
src/include/omni/graph_core.hpp | 27 +-
src/include/omni/graph_iterators.hpp | 107 +-
src/include/omni/graph_processing_algorithm.hpp | 88 +-
src/include/omni/mapping_path.hpp | 92 +-
src/include/omni/observable_graph.hpp | 72 +-
src/include/omni/omni_tools.hpp | 153 +-
src/include/omni/order_and_law.hpp | 8 +-
src/include/omni/parallel_processing.hpp | 387 ++--
src/include/omni/path_processor.hpp | 418 ++--
src/include/omni/range.hpp | 92 +
src/include/omni/relative_coverage_remover.hpp | 89 +-
src/include/omni/splitters.hpp | 10 +-
src/include/omni/tip_clipper.hpp | 78 +-
src/include/pred.hpp | 165 ++
src/include/sequence/rtseq.hpp | 6 +-
src/include/sequence/seq.hpp | 17 +-
src/include/sequence/simple_seq.hpp | 37 +-
src/include/simple_tools.hpp | 14 +
src/include/ssw/ssw.h | 138 +-
src/include/ssw/ssw_cpp.h | 50 +-
src/include/version.hpp.in | 7 +
src/io/CMakeLists.txt | 6 +-
src/io/library.cpp | 10 +-
src/io/sam/read.cpp | 42 +
src/{corrector => io/sam}/sam_reader.cpp | 20 +-
src/ionhammer/CMakeLists.txt | 2 +-
src/ionhammer/HSeq.hpp | 6 +-
src/ionhammer/main.cpp | 2 +
src/mph_index/MurmurHash3.cpp | 345 ---
src/scaffold_correction/scaffold_correction.hpp | 11 +-
src/spades_pipeline/easy_align.py | 43 +
src/spades_pipeline/hammer_logic.py | 2 +
src/spades_pipeline/options_storage.py | 61 +-
src/spades_pipeline/run_contig_breaker.py | 53 +-
src/spades_pipeline/spades_logic.py | 10 +-
src/spades_pipeline/support.py | 56 +-
.../truspades/barcode_extraction.py | 5 +-
src/spades_pipeline/truspades/break_by_coverage.py | 12 +-
src/spades_pipeline/truspades/launch_options.py | 45 +-
truspades.py | 29 +-
truspades_manual.html | 15 +-
320 files changed, 18020 insertions(+), 28941 deletions(-)
diff --cc debian/changelog
index d76ca7b,258562a..9930e63
--- a/debian/changelog
+++ b/debian/changelog
@@@ -1,9 -1,40 +1,46 @@@
+ spades (3.7.1+dfsg-2) unstable; urgency=medium
+
+ [ Sascha Steinbiss ]
+ * Use asciidoctor instead of ronn for reproducible man pages
+ * enable full hardening
+ * add override for pedantic Lintian msg
+ * use correct YAML module
+ Closes: #818584
+
+ [ Afif Elghraoui ]
+ * Replace patch with a sed command to fix python-yaml imports
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Fri, 18 Mar 2016 14:25:06 +0000
+
+ spades (3.7.1+dfsg-1) unstable; urgency=medium
+
+ * New upstream release.
+ * Add gbp.conf to always use pristine-tar.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Sat, 12 Mar 2016 07:23:31 +0000
+
+ spades (3.7.0+dfsg-1) unstable; urgency=medium
+
+ * Make changelog building reproducible.
+ * New upstream release.
+ * Update d/copyright.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Wed, 24 Feb 2016 22:02:53 +0000
+
+ spades (3.6.2+dfsg-2) unstable; urgency=medium
+
+ * Use Debian's jemalloc.
+ * Fix spelling issues.
+ * Bump Standards-Version.
+
+ -- Sascha Steinbiss <sascha at steinbiss.name> Mon, 22 Feb 2016 09:27:51 +0000
+
+spades (3.6.2+dfsg-1~ubuntu14.04~ppa1) trusty; urgency=medium
+
+ * Rebuild for Debian Med PPA
+
+ -- Andreas Tille <tille at debian.org> Wed, 17 Feb 2016 10:28:35 +0100
+
spades (3.6.2+dfsg-1) unstable; urgency=low
* Initial release (Closes: #813988)
--
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