[med-svn] [spades] branch ubuntu/trusty-backports updated (ca688fa -> e9515a6)

Sascha Steinbiss sascha at steinbiss.name
Mon Jun 13 09:39:57 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  ca688fa   add mergechangelogs attrib
      adds  dfb1bae   Set minimum version of asciidoctor build-dependency
      adds  c890006   force LANG and LANGUAGE for reproducibility
      adds  44766e6   enable compiler message output
      adds  5dac0a3   Imported Upstream version 3.8.0+dfsg
      adds  78b8a93   Merge tag 'upstream/3.8.0+dfsg'
      adds  17b7a54   update licenses
      adds  9062291   adjust patches, links
      adds  27536ea   add tests for metaspades
      adds  977ea21   update d/changelog
      adds  d0644c3   add man pages
      adds  1a5604e   add license
      adds  429336c   add patch header
      adds  afc3fcc   bump Standards-Version
      adds  a1a1aa2   use stable link order
      adds  bc265dc   Imported Upstream version 3.8.1+dfsg
      adds  d56bee1   Merge tag 'upstream/3.8.1+dfsg'
      adds  ca397f5   version bump
       new  9ab86ea   Merge branch 'master' into ubuntu/trusty-backports
       new  e9515a6   build 3.8.1 for trusty

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:
 VERSION                                            |    3 +-
 changelog.html                                     |   12 +
 .../cclean/{config.info.template => config.info}   |    0
 configs/corrector/corrector.info.template          |    7 -
 configs/debruijn/careful_mode.info                 |   37 +
 configs/debruijn/config.info                       |   42 +-
 configs/debruijn/config.info.template              |  180 --
 configs/debruijn/construction.info.template        |   23 -
 configs/debruijn/detail_info_printer.info          |    1 +
 configs/debruijn/detail_info_printer.info.template |   43 -
 configs/debruijn/diploid_mode.info                 |   16 +
 configs/debruijn/distance_estimation.info          |   59 +-
 configs/debruijn/distance_estimation.info.template |   91 -
 configs/debruijn/log.properties.template           |   52 -
 configs/debruijn/mda_mode.info                     |  120 +
 configs/debruijn/meta_mode.info                    |  171 ++
 configs/debruijn/moleculo_mode.info                |  127 +
 configs/debruijn/path_extend/pe_params.info        |   36 +-
 .../debruijn/path_extend/pe_params.info.template   |  186 --
 configs/debruijn/pe_params.info                    |  138 ++
 configs/debruijn/plasmid_mode.info                 |   12 +
 configs/debruijn/rna_mode.info                     |   75 +
 configs/debruijn/simplification.info               |  374 +--
 configs/debruijn/simplification.info.template      |  561 -----
 configs/debruijn/tsa.info.template                 |    5 -
 configs/dipspades/config.info.template             |   64 -
 configs/dipspades/log.properties.template          |   36 -
 configs/hammer/config.info.template                |   56 -
 configs/ionhammer/ionhammer.cfg.template           |   12 -
 debian/changelog                                   |   30 +
 debian/control                                     |    2 +-
 debian/copyright                                   |   26 +-
 debian/links                                       |    6 +
 debian/man_src/metaspades.1.adoc                   |   18 +
 debian/man_src/plasmidspades.1.adoc                |   18 +
 debian/man_src/spades.1.ronn                       |   12 +-
 .../0002_use_debian_packaged_python-joblib.patch   |   10 +-
 debian/patches/0003_accept-system-bwa.patch        |   12 +-
 .../0101_cmake_ignore_removed_python-yaml.patch    |   13 +-
 .../0102_cmake_ignore_removed_python-joblib.patch  |    6 +-
 debian/patches/0110_build_single_thread.patch      |    8 +-
 debian/patches/0111_use_full_config_dirs.patch     |   77 +-
 debian/patches/0113_adjust_paths.patch             |   14 +-
 debian/patches/0114_use_debian_provided_libs.patch |   42 +-
 debian/patches/0115_enable_compiler_messages.patch |   12 +
 debian/patches/0116_stable_link_order.patch        |   12 +
 debian/patches/series                              |    5 +-
 debian/rules                                       |    4 +-
 debian/tests/run-upstreams-tests                   |    2 +-
 dipspades.py                                       |   10 +-
 ext/include/htrie/ahtable.h                        |  115 +
 ext/include/htrie/common.h                         |   22 +
 ext/include/htrie/hat-trie.h                       |   74 +
 ext/include/llvm/ADT/ArrayRef.h                    |  384 +++
 ext/include/llvm/ADT/DenseMap.h                    | 1074 +++++++++
 ext/include/llvm/ADT/DenseMapInfo.h                |  221 ++
 ext/include/llvm/ADT/EpochTracker.h                |   78 +
 ext/include/llvm/ADT/FoldingSet.h                  |  750 ++++++
 ext/include/llvm/ADT/Hashing.h                     |  661 ++++++
 ext/include/llvm/ADT/IntrusiveRefCntPtr.h          |  288 +++
 ext/include/llvm/ADT/None.h                        |   26 +
 ext/include/llvm/ADT/Optional.h                    |  228 ++
 ext/include/llvm/ADT/PointerEmbeddedInt.h          |  103 +
 ext/include/llvm/ADT/PointerIntPair.h              |  223 ++
 ext/include/llvm/ADT/PointerSumType.h              |  205 ++
 ext/include/llvm/ADT/PointerUnion.h                |  474 ++++
 ext/include/llvm/ADT/STLExtras.h                   |  472 ++++
 ext/include/llvm/ADT/SmallString.h                 |  297 +++
 ext/include/llvm/ADT/SmallVector.h                 |  954 ++++++++
 ext/include/llvm/ADT/StringExtras.h                |  212 ++
 ext/include/llvm/ADT/StringMap.h                   |  463 ++++
 ext/include/llvm/ADT/StringRef.h                   |  593 +++++
 ext/include/llvm/ADT/StringSwitch.h                |  166 ++
 ext/include/llvm/ADT/Twine.h                       |  540 +++++
 ext/include/llvm/ADT/edit_distance.h               |  103 +
 ext/include/llvm/ADT/ilist.h                       |  800 +++++++
 ext/include/llvm/ADT/ilist_node.h                  |  123 +
 ext/include/llvm/ADT/iterator.h                    |  246 ++
 ext/include/llvm/ADT/iterator_range.h              |   68 +
 ext/include/llvm/Config.h.in                       |   31 +
 ext/include/llvm/Support/AlignOf.h                 |  173 ++
 ext/include/llvm/Support/Allocator.h               |  435 ++++
 ext/include/llvm/Support/Atomic.h                  |   35 +
 ext/include/llvm/Support/Casting.h                 |  326 +++
 ext/include/llvm/Support/Compiler.h                |  435 ++++
 ext/include/llvm/Support/DataTypes.h               |   56 +
 ext/include/llvm/Support/Debug.h                   |   96 +
 ext/include/llvm/Support/Errc.h                    |   86 +
 ext/include/llvm/Support/Errno.h                   |   34 +
 ext/include/llvm/Support/ErrorHandling.h           |  106 +
 ext/include/llvm/Support/ErrorOr.h                 |  298 +++
 ext/include/llvm/Support/FileOutputBuffer.h        |   89 +
 ext/include/llvm/Support/FileSystem.h              |  850 +++++++
 ext/include/llvm/Support/FileUtilities.h           |   78 +
 ext/include/llvm/Support/Format.h                  |  191 ++
 ext/include/llvm/Support/Host.h                    |   38 +
 ext/include/llvm/Support/LineIterator.h            |   88 +
 ext/include/llvm/Support/MathExtras.h              |  715 ++++++
 ext/include/llvm/Support/Memory.h                  |  186 ++
 ext/include/llvm/Support/MemoryBuffer.h            |  169 ++
 ext/include/llvm/Support/Mutex.h                   |  155 ++
 ext/include/llvm/Support/MutexGuard.h              |   41 +
 ext/include/llvm/Support/Path.h                    |  437 ++++
 ext/include/llvm/Support/PointerLikeTypeTraits.h   |   92 +
 ext/include/llvm/Support/Regex.h                   |  105 +
 ext/include/llvm/Support/SMLoc.h                   |   63 +
 ext/include/llvm/Support/Signals.h                 |   71 +
 ext/include/llvm/Support/SourceMgr.h               |  285 +++
 ext/include/llvm/Support/StringSaver.h             |   32 +
 ext/include/llvm/Support/SwapByteOrder.h           |  115 +
 ext/include/llvm/Support/UniqueLock.h              |   67 +
 ext/include/llvm/Support/YAMLParser.h              |  601 +++++
 ext/include/llvm/Support/YAMLTraits.h              | 1446 ++++++++++++
 ext/include/llvm/Support/raw_ostream.h             |  530 +++++
 ext/include/llvm/Support/type_traits.h             |  109 +
 {src => ext}/include/ssw/ssw.h                     |    0
 ext/include/ssw/ssw_cpp.h                          |  215 ++
 ext/include/yaml-cpp/anchor.h                      |   16 -
 ext/include/yaml-cpp/binary.h                      |   62 -
 ext/include/yaml-cpp/contrib/anchordict.h          |   42 -
 ext/include/yaml-cpp/contrib/graphbuilder.h        |  133 --
 ext/include/yaml-cpp/dll.h                         |   28 -
 ext/include/yaml-cpp/emitfromevents.h              |   45 -
 ext/include/yaml-cpp/emitter.h                     |  209 --
 ext/include/yaml-cpp/emitterdef.h                  |   13 -
 ext/include/yaml-cpp/emittermanip.h                |  149 --
 ext/include/yaml-cpp/eventhandler.h                |   36 -
 ext/include/yaml-cpp/exceptions.h                  |  201 --
 ext/include/yaml-cpp/mark.h                        |   26 -
 ext/include/yaml-cpp/node/convert.h                |  224 --
 ext/include/yaml-cpp/node/detail/bool_type.h       |   26 -
 ext/include/yaml-cpp/node/detail/impl.h            |  163 --
 ext/include/yaml-cpp/node/detail/iterator.h        |   64 -
 ext/include/yaml-cpp/node/detail/iterator_fwd.h    |   27 -
 ext/include/yaml-cpp/node/detail/memory.h          |   39 -
 ext/include/yaml-cpp/node/detail/node.h            |  130 --
 ext/include/yaml-cpp/node/detail/node_data.h       |  110 -
 ext/include/yaml-cpp/node/detail/node_iterator.h   |  143 --
 ext/include/yaml-cpp/node/detail/node_ref.h        |   69 -
 ext/include/yaml-cpp/node/emit.h                   |   23 -
 ext/include/yaml-cpp/node/impl.h                   |  382 ---
 ext/include/yaml-cpp/node/iterator.h               |   28 -
 ext/include/yaml-cpp/node/node.h                   |  112 -
 ext/include/yaml-cpp/node/parse.h                  |   28 -
 ext/include/yaml-cpp/node/ptr.h                    |   29 -
 ext/include/yaml-cpp/node/type.h                   |   14 -
 ext/include/yaml-cpp/noncopyable.h                 |   25 -
 ext/include/yaml-cpp/null.h                        |   25 -
 ext/include/yaml-cpp/ostream_wrapper.h             |   69 -
 ext/include/yaml-cpp/parser.h                      |   47 -
 ext/include/yaml-cpp/stlemitter.h                  |   51 -
 ext/include/yaml-cpp/traits.h                      |   57 -
 ext/include/yaml-cpp/yaml.h                        |   21 -
 ext/src/CMakeLists.txt                             |    5 +-
 .../bamtools/api/internal/bam/BamMultiReader_p.cpp |    4 +-
 ext/src/cityhash/city.cc                           |  132 --
 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/Atomic.cpp                            |   58 +
 ext/src/llvm/CMakeLists.txt                        |   37 +
 ext/src/llvm/ErrorHandling.cpp                     |  112 +
 ext/src/llvm/Hashing.cpp                           |   29 +
 ext/src/llvm/LineIterator.cpp                      |   94 +
 ext/src/llvm/MemoryBuffer.cpp                      |  401 ++++
 ext/src/llvm/Mutex.cpp                             |   93 +
 ext/src/llvm/Path.cpp                              |  911 ++++++++
 ext/src/llvm/Path.inc                              |  620 +++++
 ext/src/llvm/Regex.cpp                             |  193 ++
 ext/src/llvm/Signals.cpp                           |   62 +
 ext/src/llvm/Signals.inc                           |  435 ++++
 ext/src/llvm/SmallVector.cpp                       |   41 +
 ext/src/llvm/SourceMgr.cpp                         |  476 ++++
 ext/src/llvm/StringMap.cpp                         |  245 ++
 ext/src/llvm/StringRef.cpp                         |  445 ++++
 ext/src/llvm/Twine.cpp                             |  162 ++
 ext/src/llvm/Unix.h                                |   57 +
 ext/src/llvm/YAMLParser.cpp                        | 2445 ++++++++++++++++++++
 ext/src/llvm/YAMLTraits.cpp                        | 1021 ++++++++
 ext/src/llvm/raw_ostream.cpp                       |  752 ++++++
 ext/src/llvm/regcclass.h                           |   75 +
 ext/src/llvm/regcname.h                            |  144 ++
 ext/src/llvm/regcomp.c                             | 1568 +++++++++++++
 ext/src/llvm/regengine.inc                         | 1034 +++++++++
 ext/src/llvm/regerror.c                            |  131 ++
 ext/src/llvm/regex2.h                              |  162 ++
 ext/src/llvm/regex_impl.h                          |  108 +
 ext/src/llvm/regexec.c                             |  162 ++
 ext/src/llvm/regfree.c                             |   72 +
 ext/src/llvm/regstrlcpy.c                          |   52 +
 ext/src/llvm/regutils.h                            |   58 +
 ext/src/samtools/examples/ex1.bam                  |  Bin 126580 -> 0 bytes
 ext/src/samtools/examples/ex1.sam.gz               |  Bin 114565 -> 0 bytes
 ext/src/yaml-cpp/CMakeLists.txt                    |   14 -
 ext/src/yaml-cpp/binary.cpp                        |   93 -
 ext/src/yaml-cpp/collectionstack.h                 |   35 -
 ext/src/yaml-cpp/contrib/graphbuilder.cpp          |   16 -
 ext/src/yaml-cpp/contrib/graphbuilderadapter.cpp   |   96 -
 ext/src/yaml-cpp/contrib/graphbuilderadapter.h     |   73 -
 ext/src/yaml-cpp/convert.cpp                       |   83 -
 ext/src/yaml-cpp/directives.cpp                    |   24 -
 ext/src/yaml-cpp/directives.h                      |   29 -
 ext/src/yaml-cpp/emit.cpp                          |   29 -
 ext/src/yaml-cpp/emitfromevents.cpp                |  105 -
 ext/src/yaml-cpp/emitter.cpp                       |  951 --------
 ext/src/yaml-cpp/emitterstate.cpp                  |  384 ---
 ext/src/yaml-cpp/emitterstate.h                    |  190 --
 ext/src/yaml-cpp/emitterutils.cpp                  |  424 ----
 ext/src/yaml-cpp/emitterutils.h                    |   36 -
 ext/src/yaml-cpp/exp.cpp                           |  113 -
 ext/src/yaml-cpp/exp.h                             |  196 --
 ext/src/yaml-cpp/indentation.h                     |   38 -
 ext/src/yaml-cpp/memory.cpp                        |   29 -
 ext/src/yaml-cpp/node.cpp                          |   14 -
 ext/src/yaml-cpp/node_data.cpp                     |  302 ---
 ext/src/yaml-cpp/nodebuilder.cpp                   |  138 --
 ext/src/yaml-cpp/nodebuilder.h                     |   58 -
 ext/src/yaml-cpp/nodeevents.cpp                    |   99 -
 ext/src/yaml-cpp/nodeevents.h                      |   57 -
 ext/src/yaml-cpp/null.cpp                          |    6 -
 ext/src/yaml-cpp/ostream_wrapper.cpp               |   56 -
 ext/src/yaml-cpp/parse.cpp                         |   68 -
 ext/src/yaml-cpp/parser.cpp                        |  141 --
 ext/src/yaml-cpp/ptr_stack.h                       |   49 -
 ext/src/yaml-cpp/ptr_vector.h                      |   47 -
 ext/src/yaml-cpp/regex.cpp                         |   60 -
 ext/src/yaml-cpp/regex.h                           |   67 -
 ext/src/yaml-cpp/regeximpl.h                       |  186 --
 ext/src/yaml-cpp/scanner.cpp                       |  394 ----
 ext/src/yaml-cpp/scanner.h                         |  133 --
 ext/src/yaml-cpp/scanscalar.cpp                    |  214 --
 ext/src/yaml-cpp/scanscalar.h                      |   45 -
 ext/src/yaml-cpp/scantag.cpp                       |   84 -
 ext/src/yaml-cpp/scantag.h                         |   20 -
 ext/src/yaml-cpp/scantoken.cpp                     |  439 ----
 ext/src/yaml-cpp/setting.h                         |  105 -
 ext/src/yaml-cpp/simplekey.cpp                     |  139 --
 ext/src/yaml-cpp/singledocparser.cpp               |  387 ----
 ext/src/yaml-cpp/singledocparser.h                 |   65 -
 ext/src/yaml-cpp/stream.cpp                        |  447 ----
 ext/src/yaml-cpp/stream.h                          |   79 -
 ext/src/yaml-cpp/streamcharsource.h                |   48 -
 ext/src/yaml-cpp/stringsource.h                    |   47 -
 ext/src/yaml-cpp/tag.cpp                           |   52 -
 ext/src/yaml-cpp/tag.h                             |   28 -
 ext/src/yaml-cpp/token.h                           |   85 -
 manual.html                                        |   69 +-
 metaspades.py                                      |  951 ++++++++
 plasmidspades.py                                   |  951 ++++++++
 spades.py                                          |  122 +-
 spades_compile.sh                                  |    8 +-
 src/CMakeLists.txt                                 |   25 +-
 src/cmake/includes.cmake                           |    2 +-
 src/cmake/pack.cmake                               |    4 +-
 src/corrector/CMakeLists.txt                       |   34 -
 src/corrector/config_struct.cpp                    |   51 -
 src/corrector/config_struct.hpp                    |   33 -
 src/corrector/contig_processor.cpp                 |  302 ---
 src/corrector/contig_processor.hpp                 |   65 -
 src/corrector/dataset_processor.cpp                |  278 ---
 src/corrector/dataset_processor.hpp                |   71 -
 src/corrector/interesting_pos_processor.cpp        |  125 -
 src/corrector/main.cpp                             |   62 -
 src/debruijn/CMakeLists.txt                        |   53 -
 src/debruijn/bwa_pair_info_filler.cpp              |  407 ----
 src/debruijn/bwa_pair_info_filler.hpp              |  254 --
 src/debruijn/config_struct.cpp                     |  799 -------
 src/debruijn/config_struct.hpp                     |  641 -----
 src/debruijn/construction.cpp                      |   73 -
 src/debruijn/construction.hpp                      |   23 -
 src/debruijn/contig_output.hpp                     |  418 ----
 src/debruijn/dataset_readers.hpp                   |  122 -
 src/debruijn/debruijn debug.launch.template        |   32 -
 src/debruijn/debruijn release.launch.template      |   17 -
 src/debruijn/debruijn_data.hpp                     |  169 --
 src/debruijn/debruijn_graph.hpp                    |  110 -
 src/debruijn/debruijn_graph_constructor.hpp        |  556 -----
 src/debruijn/debruijn_stats.cpp                    |  525 -----
 src/debruijn/detail_coverage.hpp                   |  257 --
 src/debruijn/distance_estimation.cpp               |  242 --
 src/debruijn/distance_estimation.hpp               |   24 -
 src/debruijn/early_simplification.hpp              |  269 ---
 src/debruijn/edge_index.hpp                        |  113 -
 src/debruijn/gap_closer.cpp                        |  505 ----
 src/debruijn/gap_closer.hpp                        |   33 -
 src/debruijn/genome_consistance_checker.cpp        |  236 --
 src/debruijn/genome_consistance_checker.hpp        |   78 -
 src/debruijn/genome_storage.cpp                    |   45 -
 src/debruijn/genome_storage.hpp                    |   33 -
 src/debruijn/genomic_info.hpp                      |   44 -
 src/debruijn/genomic_info_filler.cpp               |  121 -
 src/debruijn/genomic_info_filler.hpp               |   23 -
 src/debruijn/genomic_quality.hpp                   |  553 -----
 src/debruijn/graph_construction.hpp                |  190 --
 src/debruijn/graph_pack.hpp                        |  154 --
 src/debruijn/graph_read_correction.hpp             |  183 --
 src/debruijn/graphio.hpp                           | 1017 --------
 src/debruijn/indices/edge_index_builders.hpp       |  179 --
 src/debruijn/indices/edge_info_updater.hpp         |   96 -
 src/debruijn/indices/edge_multi_index.hpp          |  152 --
 src/debruijn/indices/edge_position_index.hpp       |  191 --
 src/debruijn/indices/kmer_extension_index.hpp      |  413 ----
 src/debruijn/indices/kmer_splitters.hpp            |  444 ----
 src/debruijn/indices/perfect_hash_map.hpp          |  397 ----
 src/debruijn/indices/storing_traits.hpp            |   61 -
 src/debruijn/is_counter.hpp                        |  173 --
 src/debruijn/kmer_coverage_model.cpp               |  379 ---
 src/debruijn/kmer_coverage_model.hpp               |   43 -
 src/debruijn/kmer_mapper.hpp                       |  224 --
 src/debruijn/kmer_mapper_logger.hpp                |   44 -
 src/debruijn/launch.hpp                            |  117 -
 src/debruijn/long_read_mapper.hpp                  |  100 -
 src/debruijn/long_read_storage.hpp                 |  376 ---
 src/debruijn/main.cpp                              |  173 --
 src/debruijn/mismatch_correction.cpp               |   27 -
 src/debruijn/mismatch_correction.hpp               |   23 -
 src/debruijn/mismatch_shall_not_pass.hpp           |  339 ---
 src/debruijn/moleculo.hpp                          |   36 -
 src/debruijn/overlap_analysis.hpp                  |  113 -
 src/debruijn/pacbio/pac_index.hpp                  |  833 -------
 src/debruijn/pacbio/pacbio_gap_closer.hpp          |  394 ----
 src/debruijn/pacbio/pacbio_read_structures.hpp     |  326 ---
 src/debruijn/pacbio_aligning.cpp                   |  186 --
 src/debruijn/pacbio_aligning.hpp                   |   23 -
 src/debruijn/pair_info_count.cpp                   |  249 --
 src/debruijn/pair_info_count.hpp                   |   24 -
 src/debruijn/pair_info_filler.hpp                  |  119 -
 src/debruijn/pair_info_improver.hpp                |  235 --
 src/debruijn/paired_statistics.hpp                 | 1058 ---------
 src/debruijn/path_extend/bidirectional_path.cpp    |   21 -
 src/debruijn/path_extend/bidirectional_path.hpp    | 1065 ---------
 src/debruijn/path_extend/extension_chooser.hpp     | 1443 ------------
 src/debruijn/path_extend/ideal_pair_info.hpp       |  129 --
 src/debruijn/path_extend/loop_traverser.hpp        |  213 --
 src/debruijn/path_extend/next_path_searcher.hpp    | 1031 ---------
 src/debruijn/path_extend/paired_library.hpp        |  180 --
 src/debruijn/path_extend/path_extend_launch.hpp    |  851 -------
 src/debruijn/path_extend/path_extender.hpp         | 1390 -----------
 src/debruijn/path_extend/path_filter.hpp           |  134 --
 src/debruijn/path_extend/path_visualizer.hpp       |  172 --
 src/debruijn/path_extend/pe_config_struct.cpp      |  164 --
 src/debruijn/path_extend/pe_config_struct.hpp      |  243 --
 src/debruijn/path_extend/pe_io.hpp                 |  279 ---
 src/debruijn/path_extend/pe_resolver.hpp           |  518 -----
 src/debruijn/path_extend/pe_utils.hpp              |  461 ----
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 src/debruijn/path_extend/split_graph_pair_info.hpp |  449 ----
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 src/debruijn/sequence_mapper.hpp                   |  431 ----
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 src/debruijn/simplification.hpp                    |   34 -
 .../simplification/graph_simplification.hpp        |  825 -------
 .../parallel_simplification_algorithms.hpp         |  924 --------
 .../simplification/simplification_settings.hpp     |  105 -
 .../simplification/single_cell_simplification.hpp  |  110 -
 src/debruijn/split_path_constructor.hpp            |  134 --
 src/debruijn/stage.cpp                             |  133 --
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 src/debruijn/standard.hpp                          |   22 -
 src/debruijn/stats/chimera_stats.hpp               |  265 ---
 src/debruijn/stats/debruijn_stats.hpp              |  417 ----
 src/debruijn/stats/statistics.hpp                  |  272 ---
 src/debruijn/utils.hpp                             |  138 --
 src/dipspades/CMakeLists.txt                       |   27 -
 .../consensus_contigs_constructor.hpp              |  332 ---
 .../abstract_contig_corrector.hpp                  |   43 -
 .../contig_correctors/close_gaps_corrector.hpp     |  154 --
 .../equal_path_deletion_correction.hpp             |   82 -
 .../contig_correctors/incorrect_contig_remover.hpp |   43 -
 .../iterative_redundant_contigs_remover.hpp        |   94 -
 .../contig_correctors/overlap_searcher.hpp         |  541 -----
 .../contig_correctors/redundant_contig_remover.hpp |  891 -------
 .../same_edge_deletion_corrector.hpp               |   71 -
 .../mapping_contig.hpp                             |  381 ---
 .../mapping_contigs_storage.hpp                    |  114 -
 .../overlap_graph.hpp                              | 1119 ---------
 src/dipspades/dipspades.hpp                        |  265 ---
 src/dipspades/dipspades_config.cpp                 |  143 --
 src/dipspades/dipspades_config.hpp                 |   82 -
 .../conservative_regions_searcher.hpp              |  174 --
 .../conservative_regions_storage.hpp               |   44 -
 .../haplotype_assembly/contig_separation_utils.hpp |  515 -----
 .../haplotype_assembly/haplotype_assembler.hpp     |   59 -
 src/dipspades/kmer_gluing/equal_sequence_gluer.hpp |  146 --
 src/dipspades/main.cpp                             |  120 -
 .../bulge_correction_condition.hpp                 |  128 -
 .../polymorphic_bulge_remover/bulge_gluer.hpp      |   88 -
 .../bulge_paths_searcher.hpp                       |   97 -
 .../polymorphic_bulge_remover/bulge_splitter.hpp   |  497 ----
 .../complex_bulge_remover.hpp                      |  145 --
 .../diploid_bulge_finder.hpp                       |  102 -
 .../glue_direction_definer.hpp                     |   76 -
 .../gluing_vertices_definer.hpp                    |  170 --
 .../iterative_tails_gluing.hpp                     |  132 --
 .../polymorphic_bulge_remover.hpp                  |  108 -
 .../simple_bulge_remover.hpp                       |   51 -
 src/dipspades/utils/bulge_utils.hpp                |  267 ---
 src/dipspades/utils/dijkstra_utils.hpp             |  163 --
 src/dipspades/utils/edge_gluer.hpp                 |  102 -
 src/dipspades/utils/element_printers.hpp           |  108 -
 src/dipspades/utils/files_utils.cpp                |   48 -
 src/dipspades/utils/histogram.hpp                  |  104 -
 src/dipspades/utils/lcs_utils.hpp                  |  146 --
 src/dipspades/utils/path_index.hpp                 |   68 -
 src/dipspades/utils/path_routines.hpp              |  286 ---
 src/dipspades/utils/range_utils.hpp                |   57 -
 src/dipspades/utils/redundancy_map.hpp             |  235 --
 src/dipspades/utils/sequence_utils.hpp             |   36 -
 src/hammer/CMakeLists.txt                          |   36 -
 src/hammer/config_struct_hammer.cpp                |   86 -
 src/hammer/config_struct_hammer.hpp                |   89 -
 src/hammer/expander.cpp                            |   70 -
 src/hammer/hamcluster.cpp                          |  288 ---
 src/hammer/hamcluster.hpp                          |  161 --
 src/hammer/hammer_tools.cpp                        |  274 ---
 src/hammer/hammer_tools.hpp                        |   57 -
 src/hammer/kmer_cluster.cpp                        |  656 ------
 src/hammer/kmer_data.cpp                           |  569 -----
 src/hammer/kmer_data.hpp                           |  141 --
 src/hammer/kmer_stat.hpp                           |  291 ---
 src/hammer/main.cpp                                |  291 ---
 src/hammer/parallel_radix_sort.hpp                 |  592 -----
 src/hammer/quake_correct/Read.cpp                  |  824 -------
 src/hammer/quake_correct/bithash.cpp               |  388 ----
 src/hammer/quake_correct/correct.cpp               |  897 -------
 src/hammer/quake_correct/edit.cpp                  |  665 ------
 src/hammer/quake_count/quake_count.cpp             |  241 --
 src/hammer/quake_count/quake_count_17.cpp          |  238 --
 src/hammer/quake_count/quake_count_19.cpp          |  238 --
 src/hammer/quake_count/quake_count_21.cpp          |  238 --
 src/hammer/quake_count/quake_count_25.cpp          |  238 --
 src/hammer/quake_count/quake_count_29.cpp          |  238 --
 src/hammer/quake_count/quake_count_33.cpp          |  239 --
 src/hammer/quake_count/quake_count_37.cpp          |  238 --
 src/hammer/quake_count/quake_count_45.cpp          |  238 --
 src/hammer/quake_count/quake_count_55.cpp          |  240 --
 src/hammer/quake_count/quake_count_65.cpp          |  238 --
 src/hammer/quake_count/quake_count_75.cpp          |  238 --
 src/hammer/quake_count/valid_kmer_generator.hpp    |  194 --
 src/hammer/quake_enhanced/count.cpp                |  131 --
 src/hammer/quake_enhanced/count/count.cpp          |  226 --
 .../quake_enhanced/filter_trusted_enh/main.cpp     |  106 -
 src/hammer/quake_enhanced/options.cpp              |  206 --
 .../test_correction_quality/main.cpp               |  108 -
 src/hammer/valid_kmer_generator.hpp                |  200 --
 src/include/adt/array_vector.hpp                   |  625 -----
 src/include/adt/bag.hpp                            |   87 -
 src/include/adt/chained_iterator.hpp               |   76 -
 src/include/adt/concurrent_dsu.hpp                 |  296 ---
 src/include/adt/filter_iterator.hpp                |   49 -
 src/include/adt/function_traits.hpp                |   70 -
 src/include/adt/iterator_range.hpp                 |   46 -
 src/include/adt/kmer_hash_vector.hpp               |  370 ---
 src/include/adt/kmer_map.hpp                       |  942 --------
 src/include/adt/kmer_set.hpp                       |  364 ---
 src/include/adt/kmer_vector.hpp                    |  165 --
 src/include/adt/parallel_seq_vector.hpp            |  110 -
 src/include/adt/pointer_iterator.hpp               |  172 --
 src/include/adt/queue_iterator.hpp                 |  143 --
 src/include/adt/small_pod_vector.hpp               |  379 ---
 src/include/config.hpp.in                          |    2 -
 src/include/config_common.hpp                      |  199 --
 src/include/config_singl.hpp                       |   55 -
 src/include/copy_file.hpp                          |   18 -
 src/include/cpp_utils.hpp                          |   41 -
 src/include/de/conj_iterator.hpp                   |  140 --
 src/include/de/data_divider.hpp                    |  140 --
 src/include/de/distance_estimation.hpp             |  311 ---
 src/include/de/extensive_distance_estimation.hpp   |  211 --
 src/include/de/index_point.hpp                     |  455 ----
 src/include/de/insert_size_refiner.hpp             |  166 --
 src/include/de/pair_info_filters.hpp               |  271 ---
 src/include/de/paired_info.hpp                     |  863 -------
 src/include/de/paired_info_helpers.hpp             |  149 --
 src/include/de/peak_finder.hpp                     |  386 ---
 src/include/de/smoothing_distance_estimation.hpp   |  221 --
 src/include/de/weighted_distance_estimation.hpp    |  115 -
 src/include/file_limit.hpp                         |   33 -
 src/include/func.hpp                               |   69 -
 src/include/graph_print_utils.hpp                  |  328 ---
 src/include/io/bam_parser.hpp                      |   67 -
 src/include/io/bam_reader.hpp                      |  105 -
 src/include/io/binary_converter.hpp                |  295 ---
 src/include/io/binary_streams.hpp                  |  357 ---
 .../io/careful_filtering_reader_wrapper.hpp        |  183 --
 src/include/io/converting_reader_wrapper.hpp       |  120 -
 src/include/io/delegating_reader_wrapper.hpp       |   64 -
 src/include/io/easy_reader.hpp                     |  122 -
 src/include/io/fasta_fastq_gz_parser.hpp           |  165 --
 src/include/io/file_reader.hpp                     |  129 --
 src/include/io/filtering_reader_wrapper.hpp        |  148 --
 src/include/io/io_helper.hpp                       |  118 -
 src/include/io/ireader.hpp                         |  116 -
 src/include/io/ireadstream.hpp                     |  168 --
 src/include/io/is_corrupting_wrapper.hpp           |   33 -
 src/include/io/kmer_iterator.hpp                   |   54 -
 src/include/io/library.hpp                         |  392 ----
 src/include/io/mmapped_reader.hpp                  |  360 ---
 src/include/io/mmapped_writer.hpp                  |  171 --
 src/include/io/modifying_reader_wrapper.hpp        |  113 -
 src/include/io/mpmc_bounded.hpp                    |  149 --
 src/include/io/multifile_reader.hpp                |   99 -
 src/include/io/orientation.hpp                     |   93 -
 src/include/io/osequencestream.hpp                 |  367 ---
 src/include/io/paired_read.hpp                     |  186 --
 src/include/io/paired_readers.hpp                  |  251 --
 src/include/io/parser.hpp                          |  145 --
 src/include/io/rc_reader_wrapper.hpp               |  137 --
 src/include/io/read.hpp                            |  231 --
 src/include/io/read_processor.hpp                  |  200 --
 src/include/io/read_stream_vector.hpp              |  182 --
 src/include/io/sam/sam_reader.hpp                  |   49 -
 src/include/io/sequence_reader.hpp                 |   77 -
 src/include/io/single_read.hpp                     |  331 ---
 src/include/io/splitting_wrapper.hpp               |   75 -
 src/include/io/vector_reader.hpp                   |   60 -
 src/include/io/wrapper_collection.hpp              |  115 -
 src/include/levenshtein.hpp                        |  238 --
 src/include/log.hpp                                |   33 -
 src/include/logger/log_writers.hpp                 |   38 -
 src/include/logger/logger.hpp                      |  149 --
 src/include/memory_limit.hpp                       |   91 -
 src/include/mph_index/bitpair_vector.hpp           |  103 -
 src/include/mph_index/common.hpp                   |   66 -
 src/include/mph_index/hypergraph_sorter_seq.hpp    |  130 --
 src/include/mph_index/kmer_index.hpp               |  530 -----
 src/include/mph_index/mphf.hpp                     |  136 --
 src/include/omni/action_handlers.hpp               |  345 ---
 src/include/omni/basic_edge_conditions.hpp         |  268 ---
 src/include/omni/bulge_remover.hpp                 |  781 -------
 src/include/omni/complex_bulge_remover.hpp         | 1162 ----------
 src/include/omni/complex_tip_clipper.hpp           |  116 -
 .../omni/concurrent_algo/bulge_remover_factory.hpp |  100 -
 .../concurrent_algo/component_algorithm_runner.hpp |  130 --
 .../concurrent_conjugate_graph_component.hpp       |  121 -
 .../concurrent_algo/concurrent_edge_algorithm.hpp  |  193 --
 .../concurrent_algo/concurrent_graph_component.hpp |  472 ----
 .../conjugate_vertex_glued_graph.hpp               |  124 -
 .../omni/concurrent_algo/devisible_tree.hpp        |  320 ---
 .../sequential_algorihtm_factory.hpp               |   38 -
 .../omni/concurrent_algo/sequential_algorithm.hpp  |   37 -
 src/include/omni/coverage.hpp                      |  342 ---
 .../omni/dijkstra_tools/dijkstra_algorithm.hpp     |  288 ---
 .../omni/dijkstra_tools/dijkstra_helper.hpp        |  163 --
 .../omni/dijkstra_tools/dijkstra_settings.hpp      |  117 -
 .../omni/dijkstra_tools/length_calculator.hpp      |  112 -
 .../omni/dijkstra_tools/neighbours_iterator.hpp    |  164 --
 .../omni/dijkstra_tools/vertex_process_checker.hpp |   72 -
 .../omni/dijkstra_tools/vertex_put_checker.hpp     |   63 -
 src/include/omni/edge_labels_handler.hpp           |  222 --
 src/include/omni/edges_position_handler.hpp        |  208 --
 src/include/omni/erroneous_connection_remover.hpp  |  381 ---
 src/include/omni/graph_component.hpp               |  198 --
 src/include/omni/graph_core.hpp                    |  620 -----
 src/include/omni/graph_iterators.hpp               |  446 ----
 src/include/omni/graph_processing_algorithm.hpp    |  259 ---
 src/include/omni/id_track_handler.hpp              |  110 -
 src/include/omni/loop_killer.hpp                   |  218 --
 src/include/omni/loop_resolver.hpp                 |   75 -
 src/include/omni/mapping_path.hpp                  |  227 --
 src/include/omni/mf_ec_remover.hpp                 |  508 ----
 src/include/omni/observable_graph.hpp              |  497 ----
 src/include/omni/omni_tools.hpp                    |  411 ----
 src/include/omni/omni_utils.hpp                    |  586 -----
 src/include/omni/order_and_law.hpp                 |  645 ------
 src/include/omni/parallel_processing.hpp           |  289 ---
 src/include/omni/path_processor.hpp                |  441 ----
 src/include/omni/range.hpp                         |   92 -
 src/include/omni/relative_coverage_remover.hpp     |  674 ------
 src/include/omni/splitters.hpp                     |  921 --------
 src/include/omni/tip_clipper.hpp                   |  177 --
 src/include/omni/visualization/graph_colorer.hpp   |  340 ---
 src/include/omni/visualization/graph_labeler.hpp   |  304 ---
 src/include/omni/visualization/graph_printer.hpp   |  176 --
 .../visualization/printing_parameter_storage.hpp   |   81 -
 src/include/omni/visualization/vertex_linker.hpp   |   41 -
 .../omni/visualization/visualization_utils.hpp     |  210 --
 src/include/omni/visualization/visualizers.hpp     |  171 --
 src/include/path_helper.hpp                        |   74 -
 src/include/perfcounter.hpp                        |  123 -
 src/include/pred.hpp                               |  165 --
 src/include/runtime_k.hpp                          |   87 -
 src/include/segfault_handler.hpp                   |   56 -
 src/include/sequence/nucl.hpp                      |  123 -
 src/include/sequence/quality.hpp                   |   39 -
 src/include/sequence/rtseq.hpp                     |  724 ------
 src/include/sequence/seq.hpp                       |  525 -----
 src/include/sequence/sequence.hpp                  |  532 -----
 src/include/sequence/sequence_tools.hpp            |  159 --
 src/include/sequence/simple_seq.hpp                |  154 --
 src/include/simple_tools.hpp                       |  184 --
 src/include/smooth.hpp                             |  193 --
 src/include/ssw/ssw_cpp.h                          |  219 --
 src/include/standard_base.hpp                      |  142 --
 src/include/verify.hpp                             |   34 -
 src/include/xmath.h                                |  346 ---
 src/io/CMakeLists.txt                              |   20 -
 src/io/copy_file.cpp                               |  158 --
 src/io/library.cpp                                 |  179 --
 src/io/logger_impl.cpp                             |  148 --
 src/io/parser.cpp                                  |   90 -
 src/io/path_helper.cpp                             |  201 --
 src/io/sam/read.cpp                                |   42 -
 src/io/sam/sam_reader.cpp                          |   75 -
 src/ionhammer/CMakeLists.txt                       |   33 -
 src/ionhammer/HSeq.hpp                             |  289 ---
 src/ionhammer/config_struct.cpp                    |   70 -
 src/ionhammer/config_struct.hpp                    |   49 -
 src/ionhammer/err_helper_table.cpp                 |   39 -
 src/ionhammer/err_helper_table.hpp                 |  117 -
 src/ionhammer/expander.cpp                         |   60 -
 src/ionhammer/flow_space_read.hpp                  |   77 -
 src/ionhammer/hamcluster.cpp                       |  219 --
 src/ionhammer/hamcluster.hpp                       |  192 --
 src/ionhammer/kmer_data.cpp                        |  245 --
 src/ionhammer/kmer_data.hpp                        |  124 -
 src/ionhammer/main.cpp                             |  336 ---
 src/ionhammer/read_corrector.hpp                   | 1220 ----------
 src/ionhammer/seqeval/BaseHypothesisEvaluator.cpp  |  302 ---
 src/ionhammer/seqeval/TreephaserLite.cpp           |  593 -----
 src/ionhammer/subcluster.cpp                       |  135 --
 src/ionhammer/valid_hkmer_generator.hpp            |  250 --
 src/modules/CMakeLists.txt                         |   24 +
 src/modules/algorithms/CMakeLists.txt              |   11 +
 .../algorithms/dijkstra/dijkstra_algorithm.hpp     |  288 +++
 .../algorithms/dijkstra/dijkstra_helper.hpp        |  163 ++
 .../algorithms/dijkstra/dijkstra_settings.hpp      |  117 +
 .../algorithms/dijkstra/length_calculator.hpp      |  112 +
 .../algorithms/dijkstra/neighbours_iterator.hpp    |  164 ++
 .../algorithms/dijkstra/vertex_process_checker.hpp |   72 +
 .../algorithms/dijkstra/vertex_put_checker.hpp     |   63 +
 .../algorithms/genome_consistance_checker.cpp      |  238 ++
 .../algorithms/genome_consistance_checker.hpp      |   77 +
 src/modules/algorithms/graph_construction.hpp      |  179 ++
 src/modules/algorithms/graph_read_correction.hpp   |  187 ++
 src/modules/algorithms/mismatch_shall_not_pass.hpp |  344 +++
 src/modules/algorithms/path_extend/CMakeLists.txt  |   18 +
 .../algorithms/path_extend/extension_chooser.hpp   | 1511 ++++++++++++
 .../algorithms/path_extend/ideal_pair_info.hpp     |  129 ++
 .../algorithms/path_extend/loop_traverser.hpp      |  213 ++
 .../algorithms/path_extend/next_path_searcher.hpp  | 1031 +++++++++
 .../algorithms/path_extend/overlap_analysis.hpp    |  113 +
 .../algorithms/path_extend/paired_library.hpp      |  179 ++
 .../algorithms/path_extend/path_extend_launch.hpp  |  975 ++++++++
 .../algorithms/path_extend/path_extender.hpp       | 1458 ++++++++++++
 src/modules/algorithms/path_extend/path_filter.hpp |  134 ++
 .../algorithms/path_extend/path_visualizer.hpp     |  172 ++
 .../algorithms/path_extend/pe_config_struct.cpp    |  172 ++
 .../algorithms/path_extend/pe_config_struct.hpp    |  252 ++
 src/modules/algorithms/path_extend/pe_io.hpp       |  263 +++
 src/modules/algorithms/path_extend/pe_resolver.hpp |  520 +++++
 src/modules/algorithms/path_extend/pe_utils.hpp    |  462 ++++
 .../scaffolder2015/connection_condition2015.cpp    |  144 ++
 .../scaffolder2015/connection_condition2015.hpp    |   90 +
 .../scaffolder2015/extension_chooser2015.cpp       |   82 +
 .../scaffolder2015/extension_chooser2015.hpp       |   49 +
 .../path_extend/scaffolder2015/scaffold_graph.cpp  |  275 +++
 .../path_extend/scaffolder2015/scaffold_graph.hpp  |  234 ++
 .../scaffolder2015/scaffold_graph_constructor.cpp  |   77 +
 .../scaffolder2015/scaffold_graph_constructor.hpp  |    0
 .../scaffolder2015/scaffold_graph_visualizer.cpp   |   72 +
 .../scaffolder2015/scaffold_graph_visualizer.hpp   |   73 +
 .../path_extend/split_graph_pair_info.hpp          |  449 ++++
 .../algorithms}/path_extend/utils/CMakeLists.txt   |    0
 .../algorithms}/path_extend/utils/find_aligns.py   |    0
 .../path_extend/utils/find_single_threshold.py     |    0
 .../path_extend/utils/paired_info_checker.cpp      |  204 ++
 .../path_extend/utils/run_all_parametrs.py         |    0
 .../algorithms/path_extend/weight_counter.hpp      |  544 +++++
 .../algorithms/simplification/bulge_remover.hpp    |  783 +++++++
 src/modules/algorithms/simplification/cleaner.hpp  |   43 +
 .../simplification/complex_bulge_remover.hpp       | 1162 ++++++++++
 .../simplification/complex_tip_clipper.hpp         |  153 ++
 .../algorithms/simplification/compressor.hpp       |  141 ++
 .../simplification/dominated_set_finder.hpp        |  137 ++
 .../simplification/ec_threshold_finder.hpp         |  152 ++
 .../erroneous_connection_remover.hpp               |  567 +++++
 .../algorithms/simplification/mf_ec_remover.hpp    |  514 ++++
 .../parallel_simplification_algorithms.hpp         |  820 +++++++
 .../simplification/relative_coverage_remover.hpp   |  674 ++++++
 .../algorithms/simplification/tip_clipper.hpp      |  269 +++
 src/modules/assembly_graph/CMakeLists.txt          |   12 +
 .../components}/component_filters.hpp              |    0
 .../components/connected_component.cpp             |   76 +
 .../components/connected_component.hpp             |   26 +
 .../assembly_graph/components/graph_component.hpp  |  198 ++
 .../assembly_graph/components/splitters.hpp        |  921 ++++++++
 .../assembly_graph/graph_alignment/edge_index.hpp  |  112 +
 .../assembly_graph/graph_alignment/kmer_map.hpp    |  151 ++
 .../assembly_graph/graph_alignment/kmer_mapper.hpp |  234 ++
 .../graph_alignment/kmer_mapper_logger.hpp         |   45 +
 .../graph_alignment/long_read_mapper.hpp           |  190 ++
 .../graph_alignment/long_read_storage.hpp          |  376 +++
 .../graph_alignment/pacbio/pac_index.hpp           |  834 +++++++
 .../graph_alignment/pacbio/pacbio_gap_closer.hpp   |  394 ++++
 .../pacbio/pacbio_read_structures.hpp              |  326 +++
 .../graph_alignment/sequence_mapper.hpp            |  408 ++++
 .../graph_alignment/sequence_mapper_notifier.hpp   |  175 ++
 .../graph_alignment/short_read_mapper.hpp          |   98 +
 .../assembly_graph/graph_core/action_handlers.hpp  |  347 +++
 .../graph_core/basic_graph_stats.hpp               |   53 +
 .../graph_core}/construction_helper.hpp            |    0
 src/modules/assembly_graph/graph_core/coverage.hpp |  343 +++
 .../assembly_graph/graph_core/debruijn_data.hpp    |  170 ++
 .../assembly_graph/graph_core/directions.hpp       |  132 ++
 src/modules/assembly_graph/graph_core/graph.hpp    |  110 +
 .../assembly_graph/graph_core/graph_core.hpp       |  620 +++++
 .../assembly_graph/graph_core/graph_iterators.hpp  |  408 ++++
 .../assembly_graph/graph_core/observable_graph.hpp |  499 ++++
 .../assembly_graph/graph_core/order_and_law.hpp    |  644 ++++++
 .../graph_support/basic_edge_conditions.hpp        |  272 +++
 .../graph_support/basic_vertex_conditions.hpp      |   52 +
 .../assembly_graph/graph_support/chimera_stats.hpp |  266 +++
 .../assembly_graph/graph_support/comparators.hpp   |   62 +
 .../assembly_graph/graph_support/contig_output.hpp |  421 ++++
 .../graph_support/detail_coverage.hpp              |  258 +++
 .../graph_support/genomic_quality.hpp              |  554 +++++
 .../graph_support/graph_processing_algorithm.hpp   |  262 +++
 .../graph_support}/marks_and_locks.hpp             |    0
 .../graph_support/parallel_processing.hpp          |  290 +++
 .../graph_support}/scaff_supplementary.cpp         |    0
 .../graph_support/scaff_supplementary.hpp          |   77 +
 .../handlers/edge_labels_handler.hpp               |  226 ++
 .../handlers/edges_position_handler.hpp            |  207 ++
 .../assembly_graph/handlers/id_track_handler.hpp   |  110 +
 .../assembly_graph/paths/bidirectional_path.cpp    |   21 +
 .../assembly_graph/paths/bidirectional_path.hpp    | 1087 +++++++++
 src/modules/assembly_graph/paths/mapping_path.hpp  |  227 ++
 src/modules/assembly_graph/paths/path_finders.hpp  |  124 +
 .../assembly_graph/paths/path_processor.hpp        |  441 ++++
 src/modules/assembly_graph/paths/path_utils.hpp    |  128 +
 src/modules/assembly_graph/stats/picture_dump.hpp  |  426 ++++
 src/modules/assembly_graph/stats/statistics.hpp    |  273 +++
 .../debruijn_graph/debruijn_graph_constructor.hpp  |  555 +++++
 .../debruijn_graph/early_simplification.hpp        |  269 +++
 .../indices/edge_index_builders.hpp                |  179 ++
 .../data_structures/indices/edge_info_updater.hpp  |  107 +
 .../data_structures/indices/edge_multi_index.hpp   |  161 ++
 .../indices/edge_position_index.hpp                |  191 ++
 .../data_structures}/indices/editable_index.hpp    |    0
 .../data_structures}/indices/key_with_hash.hpp     |    0
 .../indices/kmer_extension_index.hpp               |  413 ++++
 .../data_structures/indices/kmer_splitters.hpp     |  445 ++++
 .../data_structures/indices/perfect_hash_map.hpp   |  396 ++++
 .../data_structures/indices/storing_traits.hpp     |   61 +
 .../data_structures}/indices/values.hpp            |    0
 .../data_structures/mph_index/CMakeLists.txt       |   13 +
 .../data_structures}/mph_index/base_hash.hpp       |    0
 .../data_structures/mph_index/bitpair_vector.cpp   |   77 +
 .../data_structures/mph_index/bitpair_vector.hpp   |   27 +
 src/modules/data_structures/mph_index/common.hpp   |   66 +
 .../data_structures}/mph_index/emphf_config.hpp    |    0
 .../data_structures}/mph_index/hypergraph.hpp      |    0
 .../mph_index/hypergraph_sorter_seq.hpp            |  130 ++
 .../data_structures/mph_index/kmer_index.hpp       |  530 +++++
 src/modules/data_structures/mph_index/mphf.hpp     |  136 ++
 .../mph_index/ranked_bitpair_vector.hpp            |    0
 .../data_structures/sequence/CMakeLists.txt        |   10 +
 .../data_structures/sequence/genome_storage.cpp    |   45 +
 .../data_structures/sequence/genome_storage.hpp    |   33 +
 src/modules/data_structures/sequence/nucl.hpp      |  123 +
 src/modules/data_structures/sequence/quality.hpp   |   39 +
 src/modules/data_structures/sequence/rtseq.hpp     |  736 ++++++
 src/modules/data_structures/sequence/runtime_k.hpp |   47 +
 src/modules/data_structures/sequence/seq.hpp       |  529 +++++
 .../data_structures}/sequence/seq_common.hpp       |    0
 src/modules/data_structures/sequence/sequence.hpp  |  542 +++++
 .../data_structures/sequence/sequence_tools.hpp    |  159 ++
 .../data_structures/sequence/simple_seq.hpp        |  154 ++
 src/modules/dev_support/CMakeLists.txt             |   13 +
 src/modules/dev_support/autocompletion.cpp         |   51 +
 src/modules/dev_support/autocompletion.hpp         |   16 +
 src/modules/dev_support/copy_file.cpp              |  158 ++
 src/modules/dev_support/copy_file.hpp              |   18 +
 src/modules/dev_support/cpp_utils.hpp              |   40 +
 src/modules/dev_support/file_limit.hpp             |   33 +
 src/modules/dev_support/func.hpp                   |   69 +
 src/modules/dev_support/log.hpp                    |   33 +
 src/modules/dev_support/logger/log_writers.hpp     |   43 +
 src/modules/dev_support/logger/logger.hpp          |  149 ++
 src/modules/dev_support/logger/logger_impl.cpp     |  148 ++
 src/modules/dev_support/md5.h                      |  393 ++++
 src/{include => modules/dev_support}/memory.hpp    |    0
 src/modules/dev_support/memory_limit.hpp           |   97 +
 .../dev_support}/openmp_wrapper.h                  |    0
 .../dev_support}/parallel_wrapper.hpp              |    0
 src/modules/dev_support/path_helper.cpp            |  249 ++
 src/modules/dev_support/path_helper.hpp            |   74 +
 src/modules/dev_support/perfcounter.hpp            |  123 +
 src/modules/dev_support/range.hpp                  |   92 +
 src/modules/dev_support/segfault_handler.hpp       |   58 +
 src/modules/dev_support/simple_tools.hpp           |  184 ++
 .../dev_support}/stacktrace.hpp                    |    0
 src/modules/dev_support/standard_base.hpp          |  140 ++
 src/modules/dev_support/verify.hpp                 |   33 +
 .../examples/ex1.glf => src/modules/empty.cpp      |    0
 src/modules/io/CMakeLists.txt                      |   16 +
 src/modules/io/dataset_support/dataset_readers.hpp |  122 +
 src/modules/io/dataset_support/read_converter.hpp  |  360 +++
 src/modules/io/graph_io/graph_print_utils.hpp      |  328 +++
 src/modules/io/kmers_io/kmer_iterator.hpp          |   54 +
 src/modules/io/kmers_io/mmapped_reader.hpp         |  396 ++++
 src/modules/io/kmers_io/mmapped_writer.hpp         |  191 ++
 src/modules/io/reads/paired_read.hpp               |  186 ++
 src/modules/io/reads/read.hpp                      |  244 ++
 src/modules/io/reads/single_read.hpp               |  334 +++
 src/modules/io/reads_io/binary_converter.hpp       |  295 +++
 src/modules/io/reads_io/binary_streams.hpp         |  357 +++
 .../reads_io/careful_filtering_reader_wrapper.hpp  |  183 ++
 .../io/reads_io/converting_reader_wrapper.hpp      |  121 +
 .../io/reads_io}/cutting_reader_wrapper.hpp        |    0
 .../io/reads_io/delegating_reader_wrapper.hpp      |   64 +
 src/modules/io/reads_io/easy_reader.hpp            |  122 +
 src/modules/io/reads_io/fasta_fastq_gz_parser.hpp  |  165 ++
 src/modules/io/reads_io/file_reader.hpp            |  129 ++
 .../io/reads_io/filtering_reader_wrapper.hpp       |  148 ++
 src/modules/io/reads_io/io_helper.hpp              |  118 +
 src/modules/io/reads_io/ireader.hpp                |  117 +
 src/modules/io/reads_io/ireadstream.hpp            |  170 ++
 src/modules/io/reads_io/is_corrupting_wrapper.hpp  |   33 +
 .../io/reads_io/modifying_reader_wrapper.hpp       |  114 +
 src/modules/io/reads_io/mpmc_bounded.hpp           |  153 ++
 src/modules/io/reads_io/multifile_reader.hpp       |   99 +
 src/modules/io/reads_io/orientation.hpp            |   93 +
 src/modules/io/reads_io/osequencestream.hpp        |  374 +++
 src/modules/io/reads_io/paired_readers.hpp         |  251 ++
 src/modules/io/reads_io/parser.cpp                 |   90 +
 src/modules/io/reads_io/parser.hpp                 |  145 ++
 src/modules/io/reads_io/rc_reader_wrapper.hpp      |  137 ++
 src/modules/io/reads_io/read_processor.hpp         |  201 ++
 src/modules/io/reads_io/read_stream_vector.hpp     |  183 ++
 src/modules/io/reads_io/sequence_reader.hpp        |   77 +
 src/modules/io/reads_io/splitting_wrapper.hpp      |   75 +
 src/modules/io/reads_io/vector_reader.hpp          |   61 +
 src/modules/io/reads_io/wrapper_collection.hpp     |  115 +
 src/modules/io/sam_io/bam_parser.hpp               |   67 +
 src/modules/io/sam_io/bam_reader.hpp               |  107 +
 src/modules/io/sam_io/read.cpp                     |   42 +
 src/{include/io/sam => modules/io/sam_io}/read.hpp |    0
 src/modules/io/sam_io/sam_reader.cpp               |   75 +
 src/modules/io/sam_io/sam_reader.hpp               |   49 +
 src/modules/math/CMakeLists.txt                    |   14 +
 src/modules/math/kmer_coverage_model.cpp           |  394 ++++
 src/modules/math/kmer_coverage_model.hpp           |   50 +
 src/modules/math/pred.hpp                          |  169 ++
 src/modules/math/smooth.hpp                        |  195 ++
 src/modules/math/xmath.h                           |  357 +++
 src/modules/paired_info/CMakeLists.txt             |   14 +
 src/modules/paired_info/bwa_pair_info_filler.cpp   |  408 ++++
 src/modules/paired_info/bwa_pair_info_filler.hpp   |  253 ++
 src/modules/paired_info/data_divider.hpp           |  137 ++
 src/modules/paired_info/distance_estimation.hpp    |  309 +++
 src/modules/paired_info/histogram.hpp              |  190 ++
 src/modules/paired_info/index_point.hpp            |  370 +++
 src/modules/paired_info/insert_size_refiner.hpp    |  165 ++
 src/modules/paired_info/is_counter.hpp             |  167 ++
 src/modules/paired_info/pair_info_bounds.hpp       |   30 +
 src/modules/paired_info/pair_info_filler.hpp       |  119 +
 src/modules/paired_info/pair_info_filters.hpp      |  271 +++
 src/modules/paired_info/pair_info_improver.hpp     |  279 +++
 src/modules/paired_info/paired_info.hpp            |  712 ++++++
 src/modules/paired_info/paired_info_helpers.hpp    |  142 ++
 src/modules/paired_info/peak_finder.hpp            |  385 +++
 .../paired_info/smoothing_distance_estimation.hpp  |  283 +++
 src/modules/paired_info/split_path_constructor.hpp |  140 ++
 .../paired_info/weighted_distance_estimation.hpp   |  112 +
 src/modules/paired_info/weights.hpp                |   82 +
 src/modules/pipeline/CMakeLists.txt                |   14 +
 src/modules/pipeline/config_common.hpp             |  140 ++
 src/modules/pipeline/config_singl.hpp              |   57 +
 src/modules/pipeline/config_struct.cpp             |  786 +++++++
 src/modules/pipeline/config_struct.hpp             |  561 +++++
 src/modules/pipeline/genomic_info.hpp              |   48 +
 src/modules/pipeline/genomic_info_filler.cpp       |  149 ++
 src/modules/pipeline/genomic_info_filler.hpp       |   23 +
 src/modules/pipeline/graph_pack.hpp                |  163 ++
 src/modules/pipeline/graphio.hpp                   | 1040 +++++++++
 src/modules/pipeline/library.cpp                   |  137 ++
 src/modules/pipeline/library.hpp                   |  365 +++
 src/modules/pipeline/library.inl                   |   64 +
 src/modules/pipeline/stage.cpp                     |  133 ++
 src/modules/pipeline/stage.hpp                     |  165 ++
 src/modules/stages/CMakeLists.txt                  |   12 +
 src/modules/stages/construction.cpp                |   69 +
 src/modules/stages/construction.hpp                |   23 +
 src/modules/stages/simplification.cpp              |  509 ++++
 src/modules/stages/simplification.hpp              |   34 +
 .../graph_simplification.hpp                       |  978 ++++++++
 .../simplification_settings.hpp                    |  105 +
 .../single_cell_simplification.hpp                 |  110 +
 src/modules/visualization/graph_colorer.hpp        |  340 +++
 src/modules/visualization/graph_labeler.hpp        |  304 +++
 src/modules/visualization/graph_printer.hpp        |  176 ++
 src/modules/visualization/position_filler.hpp      |   91 +
 .../visualization/printing_parameter_storage.hpp   |   81 +
 src/modules/visualization/vertex_linker.hpp        |   41 +
 .../visualization/visualization.hpp                |    0
 src/modules/visualization/visualization_utils.hpp  |  210 ++
 src/modules/visualization/visualizers.hpp          |  173 ++
 src/projects/CMakeLists.txt                        |   13 +
 src/projects/cap/CMakeLists.txt                    |   47 +
 src/projects/cap/assembly_compare.hpp              |  520 +++++
 src/projects/cap/assembly_problem_detection.hpp    |  453 ++++
 src/projects/cap/cap_commands.hpp                  |  731 ++++++
 src/projects/cap/cap_config_struct.hpp             |   40 +
 src/projects/cap/cap_environment.hpp               |  265 +++
 src/projects/cap/cap_environment_manager.hpp       |  493 ++++
 src/projects/cap/cap_graph_pack.hpp                |   33 +
 src/projects/cap/cap_kmer_index.hpp                |  535 +++++
 src/projects/cap/cap_logger.hpp                    |   30 +
 src/projects/cap/cap_online_visualizer.hpp         |   41 +
 src/projects/cap/colored_graph_construction.hpp    |  397 ++++
 src/projects/cap/coloring.hpp                      |  461 ++++
 src/projects/cap/compare_standard.hpp              |   47 +
 src/projects/cap/comparison_utils.hpp              |  208 ++
 src/projects/cap/coordinates_handler.hpp           | 1262 ++++++++++
 src/projects/cap/deprecated/kmer_jumper.hpp        |   73 +
 src/projects/cap/deprecated/longseq_storage.hpp    |   64 +
 src/projects/cap/deprecated/tools_deprecated.cpp   |  468 ++++
 src/projects/cap/diff_masking.hpp                  |  335 +++
 src/projects/cap/gene_analysis.hpp                 |  353 +++
 src/projects/cap/genome_correction.hpp             |  496 ++++
 src/projects/cap/graph_traversal_constraints.hpp   |   75 +
 src/projects/cap/junk_cropping_reader.hpp          |   54 +
 src/projects/cap/longseq.hpp                       |  480 ++++
 src/projects/cap/main.cpp                          |   73 +
 src/projects/cap/mosaic.hpp                        | 1101 +++++++++
 src/projects/cap/path_projector.hpp                |  445 ++++
 src/projects/cap/polynomial_hash.hpp               |  404 ++++
 src/projects/cap/repeat_masking.hpp                |  544 +++++
 src/projects/cap/serialization.hpp                 |  151 ++
 src/projects/cap/simple_indel_finder.hpp           |  382 +++
 src/projects/cap/simple_inversion_finder.hpp       |  433 ++++
 src/projects/cap/stats.hpp                         | 1502 ++++++++++++
 src/projects/cap/test_utils.hpp                    |  143 ++
 src/projects/cap/tools.cpp                         |  183 ++
 src/projects/cap/untangling.hpp                    |  345 +++
 src/projects/cap/visualization.hpp                 |  171 ++
 src/projects/corrector/CMakeLists.txt              |   34 +
 src/projects/corrector/config_struct.cpp           |   78 +
 src/projects/corrector/config_struct.hpp           |   33 +
 src/projects/corrector/contig_processor.cpp        |  306 +++
 src/projects/corrector/contig_processor.hpp        |   65 +
 src/projects/corrector/dataset_processor.cpp       |  273 +++
 src/projects/corrector/dataset_processor.hpp       |   71 +
 .../corrector/interesting_pos_processor.cpp        |  127 +
 .../corrector/interesting_pos_processor.hpp        |    0
 src/projects/corrector/main.cpp                    |   67 +
 src/{ => projects}/corrector/positional_read.cpp   |    0
 src/{ => projects}/corrector/positional_read.hpp   |    0
 src/{ => projects}/corrector/variants_table.hpp    |    0
 src/projects/dipspades/CMakeLists.txt              |   26 +
 .../consensus_contigs_constructor.hpp              |  332 +++
 .../abstract_contig_corrector.hpp                  |   43 +
 .../contig_correctors/close_gaps_corrector.hpp     |  154 ++
 .../equal_path_deletion_correction.hpp             |   82 +
 .../contig_correctors/incorrect_contig_remover.hpp |   43 +
 .../iterative_redundant_contigs_remover.hpp        |   94 +
 .../contig_correctors/overlap_searcher.hpp         |  541 +++++
 .../contig_correctors/redundant_contig_remover.hpp |  891 +++++++
 .../same_edge_deletion_corrector.hpp               |   71 +
 .../mapping_contig.hpp                             |  380 +++
 .../mapping_contigs_storage.hpp                    |  114 +
 .../overlap_graph.hpp                              | 1119 +++++++++
 src/projects/dipspades/dipspades.hpp               |  265 +++
 src/projects/dipspades/dipspades_config.cpp        |  132 ++
 src/projects/dipspades/dipspades_config.hpp        |   82 +
 .../conservative_regions_searcher.hpp              |  174 ++
 .../conservative_regions_storage.hpp               |   44 +
 .../haplotype_assembly/contig_separation_utils.hpp |  515 +++++
 .../haplotype_assembly/haplotype_assembler.hpp     |   59 +
 .../dipspades/kmer_gluing/equal_sequence_gluer.hpp |  146 ++
 src/projects/dipspades/main.cpp                    |  112 +
 .../bulge_correction_condition.hpp                 |  128 +
 .../polymorphic_bulge_remover/bulge_gluer.hpp      |   88 +
 .../bulge_paths_searcher.hpp                       |   97 +
 .../polymorphic_bulge_remover/bulge_splitter.hpp   |  497 ++++
 .../complex_bulge_remover.hpp                      |  145 ++
 .../diploid_bulge_finder.hpp                       |  102 +
 .../glue_direction_definer.hpp                     |   76 +
 .../gluing_vertices_definer.hpp                    |  170 ++
 .../iterative_tails_gluing.hpp                     |  132 ++
 .../polymorphic_bulge_remover.hpp                  |  109 +
 .../simple_bulge_remover.hpp                       |   51 +
 src/projects/dipspades/utils/bulge_utils.hpp       |  267 +++
 src/projects/dipspades/utils/dijkstra_utils.hpp    |  163 ++
 src/projects/dipspades/utils/edge_gluer.hpp        |  102 +
 src/projects/dipspades/utils/element_printers.hpp  |  108 +
 src/projects/dipspades/utils/files_utils.cpp       |   48 +
 src/{ => projects}/dipspades/utils/files_utils.hpp |    0
 src/projects/dipspades/utils/histogram.hpp         |  104 +
 src/projects/dipspades/utils/lcs_utils.hpp         |  146 ++
 src/projects/dipspades/utils/path_index.hpp        |   68 +
 src/projects/dipspades/utils/path_routines.hpp     |  285 +++
 src/projects/dipspades/utils/range_utils.hpp       |   57 +
 src/projects/dipspades/utils/redundancy_map.hpp    |  235 ++
 src/projects/dipspades/utils/sequence_utils.hpp    |   36 +
 src/projects/hammer/CMakeLists.txt                 |   36 +
 src/projects/hammer/config_struct_hammer.cpp       |   86 +
 src/projects/hammer/config_struct_hammer.hpp       |   89 +
 src/projects/hammer/expander.cpp                   |   70 +
 src/{ => projects}/hammer/expander.hpp             |    0
 .../hammer/gen_test_data/CMakeLists.txt            |    0
 src/{ => projects}/hammer/gen_test_data/main.cpp   |    0
 src/{ => projects}/hammer/globals.hpp              |    0
 src/projects/hammer/hamcluster.cpp                 |  288 +++
 src/projects/hammer/hamcluster.hpp                 |  161 ++
 .../hammer/hammer debug.launch.template            |    0
 .../hammer/hammer release.launch.template          |    0
 src/projects/hammer/hammer_tools.cpp               |  274 +++
 src/projects/hammer/hammer_tools.hpp               |   57 +
 src/projects/hammer/kmer_cluster.cpp               |  656 ++++++
 src/{ => projects}/hammer/kmer_cluster.hpp         |    0
 src/projects/hammer/kmer_data.cpp                  |  568 +++++
 src/projects/hammer/kmer_data.hpp                  |  141 ++
 src/projects/hammer/kmer_stat.hpp                  |  291 +++
 src/projects/hammer/main.cpp                       |  286 +++
 src/{ => projects}/hammer/misc/config.inp          |    0
 src/{ => projects}/hammer/misc/confignohdd.inp     |    0
 src/{ => projects}/hammer/misc/getresults.pl       |    0
 src/{ => projects}/hammer/misc/memusg              |    0
 src/{ => projects}/hammer/misc/pretty_latex.pl     |    0
 src/projects/hammer/parallel_radix_sort.hpp        |  592 +++++
 .../hammer/quake_correct/CMakeLists.txt            |    0
 src/projects/hammer/quake_correct/Read.cpp         |  824 +++++++
 src/{ => projects}/hammer/quake_correct/Read.h     |    0
 src/projects/hammer/quake_correct/bithash.cpp      |  388 ++++
 src/{ => projects}/hammer/quake_correct/bithash.h  |    0
 src/projects/hammer/quake_correct/correct.cpp      |  897 +++++++
 src/projects/hammer/quake_correct/edit.cpp         |  665 ++++++
 src/{ => projects}/hammer/quake_correct/edit.h     |    0
 src/{ => projects}/hammer/quake_correct/gzstream.C |    0
 src/{ => projects}/hammer/quake_correct/gzstream.h |    0
 .../hammer/quake_count/CMakeLists.txt              |    0
 .../hammer/quake_count/kmer_freq_info.hpp          |    0
 src/projects/hammer/quake_count/quake_count.cpp    |  241 ++
 src/projects/hammer/quake_count/quake_count_17.cpp |  238 ++
 src/projects/hammer/quake_count/quake_count_19.cpp |  238 ++
 src/projects/hammer/quake_count/quake_count_21.cpp |  238 ++
 src/projects/hammer/quake_count/quake_count_25.cpp |  238 ++
 src/projects/hammer/quake_count/quake_count_29.cpp |  238 ++
 src/projects/hammer/quake_count/quake_count_33.cpp |  239 ++
 src/projects/hammer/quake_count/quake_count_37.cpp |  238 ++
 src/projects/hammer/quake_count/quake_count_45.cpp |  238 ++
 src/projects/hammer/quake_count/quake_count_55.cpp |  240 ++
 src/projects/hammer/quake_count/quake_count_65.cpp |  238 ++
 src/projects/hammer/quake_count/quake_count_75.cpp |  238 ++
 .../hammer/quake_count/valid_kmer_generator.hpp    |  194 ++
 .../hammer/quake_enhanced/CMakeLists.txt           |    0
 .../quake_enhanced/correct_hist/CMakeLists.txt     |    0
 .../hammer/quake_enhanced/correct_hist/main.cpp    |    0
 src/projects/hammer/quake_enhanced/count.cpp       |  131 ++
 .../hammer/quake_enhanced/count/CMakeLists.txt     |    0
 src/projects/hammer/quake_enhanced/count/count.cpp |  226 ++
 .../hammer/quake_enhanced/filter_trusted.cpp       |    0
 .../quake_enhanced/filter_trusted/CMakeLists.txt   |    0
 .../hammer/quake_enhanced/filter_trusted/main.cpp  |    0
 .../filter_trusted_enh/CMakeLists.txt              |    0
 .../quake_enhanced/filter_trusted_enh/main.cpp     |  106 +
 .../quake_enhanced/generate_limits/CMakeLists.txt  |    0
 .../hammer/quake_enhanced/generate_limits/main.cpp |    0
 src/{ => projects}/hammer/quake_enhanced/main.cpp  |    0
 src/projects/hammer/quake_enhanced/options.cpp     |  206 ++
 .../hammer/quake_enhanced/options.hpp              |    0
 .../quake_enhanced/prepare_graph/CMakeLists.txt    |    0
 .../quake_enhanced/prepare_graph/prepare_graph.cpp |    0
 .../hammer/quake_enhanced/prepare_hist.cpp         |    0
 .../hammer/quake_enhanced/prepare_limits.cpp       |    0
 src/{ => projects}/hammer/quake_enhanced/quake.hpp |    0
 .../test_correction_quality/CMakeLists.txt         |    0
 .../test_correction_quality/main.cpp               |  108 +
 src/{ => projects}/hammer/read_corrector.cpp       |    0
 src/{ => projects}/hammer/read_corrector.hpp       |    0
 src/projects/hammer/valid_kmer_generator.hpp       |  200 ++
 src/projects/ionhammer/CMakeLists.txt              |   33 +
 src/projects/ionhammer/HSeq.hpp                    |  289 +++
 src/projects/ionhammer/config_struct.cpp           |   84 +
 src/projects/ionhammer/config_struct.hpp           |   49 +
 src/{ => projects}/ionhammer/consensus.hpp         |    0
 src/projects/ionhammer/err_helper_table.cpp        |   39 +
 src/projects/ionhammer/err_helper_table.hpp        |  117 +
 src/{ => projects}/ionhammer/err_helper_table.inc  |    0
 src/projects/ionhammer/expander.cpp                |   60 +
 src/{ => projects}/ionhammer/expander.hpp          |    0
 src/projects/ionhammer/flow_space_read.hpp         |   77 +
 src/projects/ionhammer/hamcluster.cpp              |  219 ++
 src/projects/ionhammer/hamcluster.hpp              |  192 ++
 src/{ => projects}/ionhammer/hkmer.hpp             |    0
 src/{ => projects}/ionhammer/hkmer_distance.hpp    |    0
 src/projects/ionhammer/kmer_data.cpp               |  245 ++
 src/projects/ionhammer/kmer_data.hpp               |  124 +
 src/projects/ionhammer/main.cpp                    |  332 +++
 src/projects/ionhammer/read_corrector.hpp          | 1220 ++++++++++
 .../ionhammer/seqeval/BaseCallerUtils.h            |    0
 .../ionhammer/seqeval/BaseHypothesisEvaluator.cpp  |  302 +++
 .../ionhammer/seqeval/BaseHypothesisEvaluator.h    |    0
 src/projects/ionhammer/seqeval/TreephaserLite.cpp  |  593 +++++
 .../ionhammer/seqeval/TreephaserLite.h             |    0
 src/projects/ionhammer/subcluster.cpp              |  135 ++
 src/{ => projects}/ionhammer/subcluster.hpp        |    0
 src/projects/ionhammer/valid_hkmer_generator.hpp   |  250 ++
 src/projects/online_vis/CMakeLists.txt             |   37 +
 src/projects/online_vis/argument_list.hpp          |  217 ++
 src/projects/online_vis/base_commands.hpp          |  503 ++++
 src/projects/online_vis/command.hpp                |  173 ++
 src/projects/online_vis/command_mapping.hpp        |   54 +
 src/projects/online_vis/debruijn_commands.hpp      |   14 +
 src/projects/online_vis/debruijn_environment.hpp   |  206 ++
 .../online_vis/debruijn_online_visualizer.hpp      |   53 +
 src/projects/online_vis/drawing_commands.hpp       |  113 +
 .../drawing_commands/draw_connected_command.hpp    |   62 +
 .../drawing_commands/draw_contig_command.hpp       |  126 +
 .../drawing_commands/draw_missasemblies.hpp        |  211 ++
 .../draw_part_of_genome_command.hpp                |  115 +
 .../drawing_commands/draw_polymorphic_regions.hpp  |  139 ++
 .../drawing_commands/draw_poorly_assembled.hpp     |  617 +++++
 .../drawing_commands/draw_position_command.hpp     |   80 +
 .../drawing_commands/drawing_command.hpp           |  100 +
 .../drawing_commands/show_position_command.hpp     |   80 +
 src/projects/online_vis/environment.hpp            |   58 +
 src/projects/online_vis/errors.hpp                 |  122 +
 src/projects/online_vis/history.hpp                |   64 +
 src/projects/online_vis/loaded_environments.hpp    |   17 +
 src/projects/online_vis/main.cpp                   |   71 +
 src/projects/online_vis/online_visualizer.hpp      |  167 ++
 src/projects/online_vis/position_commands.hpp      |   11 +
 .../position_commands/clear_position_command.hpp   |   35 +
 .../position_commands/fill_position_command.hpp    |   65 +
 src/projects/online_vis/processing_commands.hpp    |   66 +
 src/projects/online_vis/setting_commands.hpp       |  161 ++
 src/projects/online_vis/standard_vis.hpp           |   23 +
 src/projects/online_vis/statistics_commands.hpp    |   13 +
 .../junction_sequence_command.hpp                  |   97 +
 .../statistics_commands/print_contigs_stats.hpp    |  220 ++
 .../statistics_commands/print_edge_command.hpp     |   60 +
 .../statistics_commands/print_paths_command.hpp    |  103 +
 src/projects/online_vis/vis_logger.hpp             |   28 +
 src/projects/online_vis/vis_utils.hpp              |   40 +
 src/projects/scaffold_correction/CMakeLists.txt    |   23 +
 src/projects/scaffold_correction/main.cpp          |  112 +
 .../scaffold_correction/scaffold_correction.hpp    |  333 +++
 src/projects/spades/CMakeLists.txt                 |   32 +
 src/projects/spades/chromosome_removal.cpp         |  261 +++
 src/projects/spades/chromosome_removal.hpp         |   35 +
 src/projects/spades/distance_estimation.cpp        |  231 ++
 src/projects/spades/distance_estimation.hpp        |   24 +
 src/projects/spades/gap_closer.cpp                 |  502 ++++
 src/projects/spades/gap_closer.hpp                 |   33 +
 src/projects/spades/launch.hpp                     |  124 +
 src/projects/spades/main.cpp                       |  111 +
 src/projects/spades/mismatch_correction.cpp        |   27 +
 src/projects/spades/mismatch_correction.hpp        |   23 +
 src/projects/spades/pacbio_aligning.cpp            |  185 ++
 src/projects/spades/pacbio_aligning.hpp            |   23 +
 src/projects/spades/pair_info_count.cpp            |  259 +++
 src/projects/spades/pair_info_count.hpp            |   24 +
 src/projects/spades/repeat_resolving.cpp           |   96 +
 src/projects/spades/repeat_resolving.hpp           |   42 +
 src/projects/spades/second_phase_setup.cpp         |   42 +
 src/projects/spades/second_phase_setup.hpp         |   22 +
 .../truseq_analysis/AlignmentAnalyserNew.cpp       |  102 +
 .../truseq_analysis/AlignmentAnalyserNew.hpp       |   34 +
 src/projects/truseq_analysis/CMakeLists.txt        |   15 +
 .../truseq_analysis/alignment_analyser.cpp         |  116 +
 .../truseq_analysis/alignment_analyser.hpp         |   41 +
 src/projects/truseq_analysis/analysis_pipeline.cpp |  140 ++
 src/projects/truseq_analysis/analysis_pipeline.hpp |   39 +
 .../truseq_analysis/consistent_mapping.cpp         |  245 ++
 src/projects/truseq_analysis/consistent_mapping.h  |   90 +
 src/projects/truseq_analysis/main.cpp              |   95 +
 src/scaffold_correction/CMakeLists.txt             |   24 -
 src/scaffold_correction/main.cpp                   |  171 --
 src/scaffold_correction/scaffold_correction.hpp    |  332 ---
 src/spades_pipeline/corrector_logic.py             |   11 +-
 src/spades_pipeline/dipspades_logic.py             |    3 -
 src/spades_pipeline/hammer_logic.py                |   85 +-
 src/spades_pipeline/options_storage.py             |   52 +-
 src/spades_pipeline/spades_logic.py                |  104 +-
 src/spades_pipeline/support.py                     |   83 +-
 src/spades_pipeline/truspades/launch_options.py    |   10 +-
 src/utils/adt/array_vector.hpp                     |  677 ++++++
 src/utils/adt/bag.hpp                              |   87 +
 src/utils/adt/chained_iterator.hpp                 |   76 +
 src/utils/adt/concurrent_dsu.hpp                   |  297 +++
 src/utils/adt/filter_iterator.hpp                  |   49 +
 src/{include => utils}/adt/flat_map.hpp            |    0
 src/{include => utils}/adt/flat_set.hpp            |    0
 src/utils/adt/function_traits.hpp                  |   76 +
 src/utils/adt/iterator_range.hpp                   |   50 +
 src/utils/adt/kmer_hash_vector.hpp                 |  370 +++
 src/utils/adt/kmer_vector.hpp                      |  179 ++
 src/utils/adt/parallel_seq_vector.hpp              |  110 +
 .../adt/parallel_unordered_map.hpp                 |    0
 src/utils/adt/pointer_iterator.hpp                 |  174 ++
 src/utils/adt/queue_iterator.hpp                   |  143 ++
 src/utils/adt/small_pod_vector.hpp                 |  399 ++++
 src/utils/levenshtein.hpp                          |  241 ++
 truspades.py                                       |   21 +-
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 create mode 100644 src/projects/online_vis/vis_utils.hpp
 create mode 100644 src/projects/scaffold_correction/CMakeLists.txt
 create mode 100644 src/projects/scaffold_correction/main.cpp
 create mode 100644 src/projects/scaffold_correction/scaffold_correction.hpp
 create mode 100644 src/projects/spades/CMakeLists.txt
 create mode 100644 src/projects/spades/chromosome_removal.cpp
 create mode 100644 src/projects/spades/chromosome_removal.hpp
 create mode 100644 src/projects/spades/distance_estimation.cpp
 create mode 100644 src/projects/spades/distance_estimation.hpp
 create mode 100644 src/projects/spades/gap_closer.cpp
 create mode 100644 src/projects/spades/gap_closer.hpp
 create mode 100644 src/projects/spades/launch.hpp
 create mode 100644 src/projects/spades/main.cpp
 create mode 100644 src/projects/spades/mismatch_correction.cpp
 create mode 100644 src/projects/spades/mismatch_correction.hpp
 create mode 100644 src/projects/spades/pacbio_aligning.cpp
 create mode 100644 src/projects/spades/pacbio_aligning.hpp
 create mode 100644 src/projects/spades/pair_info_count.cpp
 create mode 100644 src/projects/spades/pair_info_count.hpp
 create mode 100644 src/projects/spades/repeat_resolving.cpp
 create mode 100644 src/projects/spades/repeat_resolving.hpp
 create mode 100644 src/projects/spades/second_phase_setup.cpp
 create mode 100644 src/projects/spades/second_phase_setup.hpp
 create mode 100644 src/projects/truseq_analysis/AlignmentAnalyserNew.cpp
 create mode 100644 src/projects/truseq_analysis/AlignmentAnalyserNew.hpp
 create mode 100644 src/projects/truseq_analysis/CMakeLists.txt
 create mode 100644 src/projects/truseq_analysis/alignment_analyser.cpp
 create mode 100644 src/projects/truseq_analysis/alignment_analyser.hpp
 create mode 100644 src/projects/truseq_analysis/analysis_pipeline.cpp
 create mode 100644 src/projects/truseq_analysis/analysis_pipeline.hpp
 create mode 100644 src/projects/truseq_analysis/consistent_mapping.cpp
 create mode 100644 src/projects/truseq_analysis/consistent_mapping.h
 create mode 100644 src/projects/truseq_analysis/main.cpp
 delete mode 100644 src/scaffold_correction/CMakeLists.txt
 delete mode 100644 src/scaffold_correction/main.cpp
 delete mode 100644 src/scaffold_correction/scaffold_correction.hpp
 create mode 100644 src/utils/adt/array_vector.hpp
 create mode 100644 src/utils/adt/bag.hpp
 create mode 100644 src/utils/adt/chained_iterator.hpp
 create mode 100644 src/utils/adt/concurrent_dsu.hpp
 create mode 100644 src/utils/adt/filter_iterator.hpp
 rename src/{include => utils}/adt/flat_map.hpp (100%)
 rename src/{include => utils}/adt/flat_set.hpp (100%)
 create mode 100644 src/utils/adt/function_traits.hpp
 create mode 100644 src/utils/adt/iterator_range.hpp
 create mode 100644 src/utils/adt/kmer_hash_vector.hpp
 create mode 100644 src/utils/adt/kmer_vector.hpp
 create mode 100644 src/utils/adt/parallel_seq_vector.hpp
 rename src/{include => utils}/adt/parallel_unordered_map.hpp (100%)
 create mode 100644 src/utils/adt/pointer_iterator.hpp
 create mode 100644 src/utils/adt/queue_iterator.hpp
 create mode 100644 src/utils/adt/small_pod_vector.hpp
 create mode 100644 src/utils/levenshtein.hpp

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