[med-svn] [spades] branch upstream updated (e724c2d -> 31a083f)
Sascha Steinbiss
sascha at steinbiss.name
Wed Feb 24 22:08:46 UTC 2016
This is an automated email from the git hooks/post-receive script.
sascha-guest pushed a change to branch upstream
in repository spades.
from e724c2d Imported Upstream version 3.6.2+dfsg
new 5546f51 Imported Upstream version 3.7.0+dfsg
new 31a083f Imported Upstream version 3.7.0+dfsg
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:
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
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 +-
299 files changed, 17428 insertions(+), 28610 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%)
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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