[med-svn] [spades] branch ubuntu/trusty-backports updated (c2bbc53 -> ca688fa)
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 change to branch ubuntu/trusty-backports
in repository spades.
from c2bbc53 Rebuild for Debian Med PPA
adds 2c1bb88 src/io/logger_impl.cpp: add define to keep jemalloc function names
adds b28cec0 fix spelling
adds 31207d8 bump Standards-Version
adds 7014189 use Debian provided jemalloc
adds 81a29b7 update changelog
adds 29b1444 dch -r
adds 6abd0e2 make build reproducible
adds 5546f51 Imported Upstream version 3.7.0+dfsg
adds 7fb6cc5 Merge tag 'upstream/3.7.0+dfsg'
adds 31a083f Imported Upstream version 3.7.0+dfsg
adds cc8a41f Merge tag 'upstream/3.7.0+dfsg'
adds 3ea0a59 new upstream release
adds 5a4f1e4 adjust s/copyright: remove MurmurHash
adds 032e5c0 dch -r
adds a93a129 Imported Upstream version 3.7.1+dfsg
adds 304c429 Merge tag 'upstream/3.7.1+dfsg'
adds ae744f6 new upstream version
adds 1e37f1b always use pristine-tar
adds 6d53a34 switch manpage building to asciidoctor
adds 58f5231 enable full hardening
adds 0551a97 add override
adds 7ce3024 use Debian packaged YAML module
adds f8c160f Use a sed command to fix yaml import statements to use the Debian package
adds 8ff60e0 Update email address
adds 3bdfebf spades (3.7.1+dfsg-2) unstable; urgency=medium
new dd546f7 Merge branch 'master' into ubuntu/trusty-backports
new 5d623b2 Revert "switch manpage building to asciidoctor"
new 0356f8a update d/changelog
new ca688fa add mergechangelogs attrib
The 4 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:
.gitattributes | 1 +
LICENSE | 16 +-
README | 14 +-
VERSION | 2 +-
changelog.html | 18 +-
.../{corrector.info.template => corrector.info} | 0
.../debruijn/{config.info.template => config.info} | 23 +-
configs/debruijn/config.info.template | 23 +-
...onstruction.info.template => construction.info} | 0
configs/debruijn/coverage_based_rr.info.template | 13 -
configs/debruijn/detail_info_printer.info | 43 +
configs/debruijn/detail_info_printer.info.template | 47 +-
...tion.info.template => distance_estimation.info} | 0
.../{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.template => tsa.info} | 0
.../{config.info.template => config.info} | 0
.../{log.properties.template => log.properties} | 0
.../hammer/{config.info.template => config.info} | 4 +-
configs/hammer/config.info.template | 4 +-
.../{ionhammer.cfg.template => ionhammer.cfg} | 0
debian/changelog | 45 +
debian/control | 8 +-
debian/copyright | 58 +-
debian/gbp.conf | 2 +
.../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 | 8 +-
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 +-
318 files changed, 17696 insertions(+), 28811 deletions(-)
create mode 100644 .gitattributes
copy configs/corrector/{corrector.info.template => corrector.info} (100%)
copy configs/debruijn/{config.info.template => config.info} (91%)
copy configs/debruijn/{construction.info.template => construction.info} (100%)
delete mode 100644 configs/debruijn/coverage_based_rr.info.template
create mode 100644 configs/debruijn/detail_info_printer.info
copy configs/debruijn/{distance_estimation.info.template => distance_estimation.info} (100%)
copy configs/debruijn/{log.properties.template => log.properties} (84%)
create mode 100644 configs/debruijn/path_extend/pe_params.info
create mode 100644 configs/debruijn/simplification.info
copy configs/debruijn/{tsa.info.template => tsa.info} (100%)
copy configs/dipspades/{config.info.template => config.info} (100%)
copy configs/dipspades/{log.properties.template => log.properties} (100%)
copy configs/hammer/{config.info.template => config.info} (90%)
copy configs/ionhammer/{ionhammer.cfg.template => ionhammer.cfg} (100%)
create mode 100644 debian/gbp.conf
delete mode 100644 debian/patches/0001_use_debian_packaged_python-yaml.patch
create mode 100644 debian/patches/0114_use_debian_provided_libs.patch
create mode 100644 debian/patches/0120_dont_rename_jemalloc_functionnames.patch
create mode 100644 debian/source.lintian-overrides
create mode 100644 ext/include/city/city.h
create mode 100644 ext/include/city/citycrc.h
delete mode 100644 ext/include/jemalloc/internal/arena.h
delete mode 100644 ext/include/jemalloc/internal/atomic.h
delete mode 100644 ext/include/jemalloc/internal/base.h
delete mode 100644 ext/include/jemalloc/internal/bitmap.h
delete mode 100644 ext/include/jemalloc/internal/chunk.h
delete mode 100644 ext/include/jemalloc/internal/chunk_dss.h
delete mode 100644 ext/include/jemalloc/internal/chunk_mmap.h
delete mode 100644 ext/include/jemalloc/internal/ckh.h
delete mode 100644 ext/include/jemalloc/internal/ctl.h
delete mode 100644 ext/include/jemalloc/internal/extent.h
delete mode 100644 ext/include/jemalloc/internal/hash.h
delete mode 100644 ext/include/jemalloc/internal/huge.h
delete mode 100644 ext/include/jemalloc/internal/jemalloc_internal.h
delete mode 100644 ext/include/jemalloc/internal/mb.h
delete mode 100644 ext/include/jemalloc/internal/mutex.h
delete mode 100644 ext/include/jemalloc/internal/private_namespace.h
delete mode 100644 ext/include/jemalloc/internal/prng.h
delete mode 100644 ext/include/jemalloc/internal/prof.h
delete mode 100644 ext/include/jemalloc/internal/ql.h
delete mode 100644 ext/include/jemalloc/internal/qr.h
delete mode 100644 ext/include/jemalloc/internal/quarantine.h
delete mode 100644 ext/include/jemalloc/internal/rb.h
delete mode 100644 ext/include/jemalloc/internal/rtree.h
delete mode 100644 ext/include/jemalloc/internal/size_classes.h
delete mode 100755 ext/include/jemalloc/internal/size_classes.sh
delete mode 100644 ext/include/jemalloc/internal/stats.h
delete mode 100644 ext/include/jemalloc/internal/tcache.h
delete mode 100644 ext/include/jemalloc/internal/tsd.h
delete mode 100644 ext/include/jemalloc/internal/util.h
delete mode 100644 ext/include/jemalloc/jemalloc.h.in
delete mode 100644 ext/include/jemalloc/jemalloc_defs.h.in
create mode 100644 ext/include/llvm/AlignOf.h
create mode 100644 ext/include/llvm/PointerEmbeddedInt.h
create mode 100644 ext/include/llvm/PointerIntPair.h
create mode 100644 ext/include/llvm/PointerLikeTypeTraits.h
create mode 100644 ext/include/llvm/PointerSumType.h
rename {src/mph_index => ext/src/cityhash}/CMakeLists.txt (64%)
create mode 100644 ext/src/cityhash/city.cc
delete mode 100644 ext/src/jemalloc/CMakeLists.txt
delete mode 100644 ext/src/jemalloc/COPYING
delete mode 100644 ext/src/jemalloc/arena.c
delete mode 100644 ext/src/jemalloc/atomic.c
delete mode 100644 ext/src/jemalloc/base.c
delete mode 100644 ext/src/jemalloc/bitmap.c
delete mode 100644 ext/src/jemalloc/chunk.c
delete mode 100644 ext/src/jemalloc/chunk_dss.c
delete mode 100644 ext/src/jemalloc/chunk_mmap.c
delete mode 100644 ext/src/jemalloc/ckh.c
delete mode 100644 ext/src/jemalloc/cmake/CheckPageSize.c.in
delete mode 100644 ext/src/jemalloc/ctl.c
delete mode 100644 ext/src/jemalloc/extent.c
delete mode 100644 ext/src/jemalloc/hash.c
delete mode 100644 ext/src/jemalloc/huge.c
delete mode 100644 ext/src/jemalloc/intercept.inl
delete mode 100644 ext/src/jemalloc/jemalloc.c
delete mode 100644 ext/src/jemalloc/mb.c
delete mode 100644 ext/src/jemalloc/mutex.c
delete mode 100644 ext/src/jemalloc/prof.c
delete mode 100644 ext/src/jemalloc/quarantine.c
delete mode 100644 ext/src/jemalloc/rtree.c
delete mode 100644 ext/src/jemalloc/stats.c
delete mode 100644 ext/src/jemalloc/tcache.c
delete mode 100644 ext/src/jemalloc/tsd.c
delete mode 100644 ext/src/jemalloc/util.c
delete mode 100644 ext/src/jemalloc/zone.c
delete mode 100644 src/corrector/read.cpp
create mode 100644 src/debruijn/bwa_pair_info_filler.cpp
create mode 100644 src/debruijn/bwa_pair_info_filler.hpp
create mode 100644 src/debruijn/genome_consistance_checker.cpp
create mode 100644 src/debruijn/genome_storage.cpp
create mode 100644 src/debruijn/genome_storage.hpp
delete mode 100644 src/debruijn/graph_simplification.hpp
create mode 100644 src/debruijn/overlap_analysis.hpp
create mode 100644 src/debruijn/path_extend/scaffolder2015/connection_condition2015.cpp
create mode 100644 src/debruijn/path_extend/scaffolder2015/connection_condition2015.hpp
create mode 100644 src/debruijn/path_extend/scaffolder2015/extension_chooser2015.cpp
create mode 100644 src/debruijn/path_extend/scaffolder2015/extension_chooser2015.hpp
create mode 100644 src/debruijn/path_extend/scaffolder2015/scaff_supplementary.cpp
create mode 100644 src/debruijn/path_extend/scaffolder2015/scaff_supplementary.hpp
create mode 100644 src/debruijn/path_extend/scaffolder2015/scaffold_graph.cpp
create mode 100644 src/debruijn/path_extend/scaffolder2015/scaffold_graph.hpp
create mode 100644 src/debruijn/path_extend/scaffolder2015/scaffold_graph_constructor.cpp
create mode 100644 src/debruijn/path_extend/scaffolder2015/scaffold_graph_constructor.hpp
create mode 100644 src/debruijn/path_extend/scaffolder2015/scaffold_graph_visualizer.cpp
create mode 100644 src/debruijn/path_extend/scaffolder2015/scaffold_graph_visualizer.hpp
delete mode 100644 src/debruijn/repeat.hpp
create mode 100644 src/debruijn/simplification/graph_simplification.hpp
create mode 100644 src/debruijn/simplification/single_cell_simplification.hpp
create mode 100644 src/include/adt/flat_map.hpp
create mode 100644 src/include/adt/flat_set.hpp
create mode 100644 src/include/adt/function_traits.hpp
create mode 100644 src/include/adt/small_pod_vector.hpp
create mode 100644 src/include/de/conj_iterator.hpp
create mode 100644 src/include/de/index_point.hpp
create mode 100644 src/include/de/paired_info_helpers.hpp
create mode 100644 src/include/io/kmer_iterator.hpp
rename src/{corrector => include/io/sam}/read.hpp (50%)
rename src/{corrector => include/io/sam}/sam_reader.hpp (93%)
delete mode 100644 src/include/mph_index/MurmurHash3.h
create mode 100644 src/include/omni/range.hpp
create mode 100644 src/include/pred.hpp
create mode 100644 src/include/version.hpp.in
create mode 100644 src/io/sam/read.cpp
rename src/{corrector => io/sam}/sam_reader.cpp (82%)
delete mode 100644 src/mph_index/MurmurHash3.cpp
create mode 100755 src/spades_pipeline/easy_align.py
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