[med-svn] [spades] branch master updated (6abd0e2 -> 032e5c0)
Sascha Steinbiss
sascha at steinbiss.name
Wed Feb 24 22:08:23 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a change to branch master
in repository spades.
from 6abd0e2 make build reproducible
new 5546f51 Imported Upstream version 3.7.0+dfsg
new 7fb6cc5 Merge tag 'upstream/3.7.0+dfsg'
new 31a083f Imported Upstream version 3.7.0+dfsg
new cc8a41f Merge tag 'upstream/3.7.0+dfsg'
new 3ea0a59 new upstream release
new 5a4f1e4 adjust s/copyright: remove MurmurHash
new 032e5c0 dch -r
The 7 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:
LICENSE | 16 +-
README | 14 +-
VERSION | 2 +-
changelog.html | 8 +
.../{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
...sed_rr.info.template => coverage_based_rr.info} | 0
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 | 8 +-
debian/copyright | 56 +-
.../0001_use_debian_packaged_python-yaml.patch | 8 +-
debian/patches/0003_accept-system-bwa.patch | 4 +-
.../0101_cmake_ignore_removed_python-yaml.patch | 2 +-
debian/patches/0111_use_full_config_dirs.patch | 6 +-
debian/patches/0112_spelling.patch | 13 +-
debian/patches/0113_adjust_paths.patch | 35 +-
...c.patch => 0114_use_debian_provided_libs.patch} | 24 +-
debian/patches/series | 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 | 4 +-
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 +-
309 files changed, 17520 insertions(+), 28676 deletions(-)
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%)
rename configs/debruijn/{coverage_based_rr.info.template => coverage_based_rr.info} (100%)
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%)
rename debian/patches/{0114_use_debian_provided_jemalloc.patch => 0114_use_debian_provided_libs.patch} (94%)
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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