Temporary header file '/tmp/NyLyVFOGg0/dump1.h' with the following content will be compiled to create GCC translation unit dump:

  // add defines
  #define __STDC_VERSION__ 201710L
#define _GXX_NULLPTR_T
#define CLUTTER_ENABLE_COMPOSITOR_API 1
#define _REGEX_NELTS(n)
#define _Atomic
#define PACKED
#define getaddrinfo_a(a,b,c,d)

  // add includes
  #include "/usr/include/libMems/AbstractGappedAlignment.h"
  #include "/usr/include/libMems/AbstractMatch.h"
  #include "/usr/include/libMems/Aligner.h"
  #include "/usr/include/libMems/Backbone.h"
  #include "/usr/include/libMems/CompactGappedAlignment.h"
  #include "/usr/include/libMems/DNAFileSML.h"
  #include "/usr/include/libMems/DNAMemorySML.h"
  #include "/usr/include/libMems/DenseAbstractMatch.h"
  #include "/usr/include/libMems/DistanceMatrix.h"
  #include "/usr/include/libMems/FileSML.h"
  #include "/usr/include/libMems/Files.h"
  #include "/usr/include/libMems/GappedAligner.h"
  #include "/usr/include/libMems/GappedAlignment.h"
  #include "/usr/include/libMems/GreedyBreakpointElimination.h"
  #include "/usr/include/libMems/HomologyHMM/algebras.h"
  #include "/usr/include/libMems/HomologyHMM/dptables.h"
  #include "/usr/include/libMems/HomologyHMM/homology.h"
  #include "/usr/include/libMems/HomologyHMM/parameters.h"
  #include "/usr/include/libMems/HybridAbstractMatch.h"
  #include "/usr/include/libMems/Interval.h"
  #include "/usr/include/libMems/IntervalList.h"
  #include "/usr/include/libMems/Islands.h"
  #include "/usr/include/libMems/LCB.h"
  #include "/usr/include/libMems/MaskedMemHash.h"
  #include "/usr/include/libMems/Match.h"
  #include "/usr/include/libMems/MatchFinder.h"
  #include "/usr/include/libMems/MatchHashEntry.h"
  #include "/usr/include/libMems/MatchList.h"
  #include "/usr/include/libMems/MatchProjectionAdapter.h"
  #include "/usr/include/libMems/Matrix.h"
  #include "/usr/include/libMems/MemHash.h"
  #include "/usr/include/libMems/Memory.h"
  #include "/usr/include/libMems/MemorySML.h"
  #include "/usr/include/libMems/MuscleInterface.h"
  #include "/usr/include/libMems/NumericMatrix.h"
  #include "/usr/include/libMems/PairwiseMatchAdapter.h"
  #include "/usr/include/libMems/PairwiseMatchFinder.h"
  #include "/usr/include/libMems/PhyloTree.h"
  #include "/usr/include/libMems/ProgressiveAligner.h"
  #include "/usr/include/libMems/RepeatHash.h"
  #include "/usr/include/libMems/RepeatMatch.h"
  #include "/usr/include/libMems/RepeatMatchList.h"
  #include "/usr/include/libMems/Scoring.h"
  #include "/usr/include/libMems/SeedMasks.h"
  #include "/usr/include/libMems/SeedOccurrenceList.h"
  #include "/usr/include/libMems/SlotAllocator.h"
  #include "/usr/include/libMems/SortedMerList.h"
  #include "/usr/include/libMems/SparseAbstractMatch.h"
  #include "/usr/include/libMems/SubstitutionMatrix.h"
  #include "/usr/include/libMems/SuperInterval.h"
  #include "/usr/include/libMems/TreeUtilities.h"
  #include "/usr/include/libMems/UngappedLocalAlignment.h"
  #include "/usr/include/libMems/configuration.h"
  #include "/usr/include/libMems/dmSML/aPOSIXaio.h"
  #include "/usr/include/libMems/dmSML/alibc.h"
  #include "/usr/include/libMems/dmSML/alinuxaio.h"
  #include "/usr/include/libMems/dmSML/asyncio.h"
  #include "/usr/include/libMems/dmSML/awin32aio.h"
  #include "/usr/include/libMems/dmSML/buffer.h"
  #include "/usr/include/libMems/dmSML/dmsort.h"
  #include "/usr/include/libMems/dmSML/sml.h"
  #include "/usr/include/libMems/dmSML/sorting.h"
  #include "/usr/include/libMems/dmSML/timing.h"
  #include "/usr/include/libMems/dmSML/util.h"
  #include "/usr/include/libMems/gnAlignedSequences.h"
  #include "/usr/include/libMems/gnRAWSequence.h"
  #include "/usr/include/libMems/twister.h"

  // add namespaces
  namespace boost{typedef int tmp_add_type_1;}
  boost::tmp_add_type_1 tmp_add_func_1(){return 0;};
  namespace boost{namespace algorithm{typedef int tmp_add_type_2;}}
  boost::algorithm::tmp_add_type_2 tmp_add_func_2(){return 0;};
  namespace boost{namespace algorithm{namespace detail{typedef int tmp_add_type_3;}}}
  boost::algorithm::detail::tmp_add_type_3 tmp_add_func_3(){return 0;};
  namespace boost{namespace concepts{typedef int tmp_add_type_4;}}
  boost::concepts::tmp_add_type_4 tmp_add_func_4(){return 0;};
  namespace boost{namespace concepts{namespace detail{typedef int tmp_add_type_5;}}}
  boost::concepts::detail::tmp_add_type_5 tmp_add_func_5(){return 0;};
  namespace boost{namespace core{typedef int tmp_add_type_6;}}
  boost::core::tmp_add_type_6 tmp_add_func_6(){return 0;};
  namespace boost{namespace detail{typedef int tmp_add_type_7;}}
  boost::detail::tmp_add_type_7 tmp_add_func_7(){return 0;};
  namespace boost{namespace detail{namespace function{typedef int tmp_add_type_8;}}}
  boost::detail::function::tmp_add_type_8 tmp_add_func_8(){return 0;};
  namespace boost{namespace details{typedef int tmp_add_type_9;}}
  boost::details::tmp_add_type_9 tmp_add_func_9(){return 0;};
  namespace boost{namespace details{namespace pool{typedef int tmp_add_type_10;}}}
  boost::details::pool::tmp_add_type_10 tmp_add_func_10(){return 0;};
  namespace boost{namespace filesystem{typedef int tmp_add_type_11;}}
  boost::filesystem::tmp_add_type_11 tmp_add_func_11(){return 0;};
  namespace boost{namespace filesystem{namespace detail{typedef int tmp_add_type_12;}}}
  boost::filesystem::detail::tmp_add_type_12 tmp_add_func_12(){return 0;};
  namespace boost{namespace functional{typedef int tmp_add_type_13;}}
  boost::functional::tmp_add_type_13 tmp_add_func_13(){return 0;};
  namespace boost{namespace functional{namespace detail{typedef int tmp_add_type_14;}}}
  boost::functional::detail::tmp_add_type_14 tmp_add_func_14(){return 0;};
  namespace boost{namespace integer{typedef int tmp_add_type_15;}}
  boost::integer::tmp_add_type_15 tmp_add_func_15(){return 0;};
  namespace boost{namespace integer{namespace detail{typedef int tmp_add_type_16;}}}
  boost::integer::detail::tmp_add_type_16 tmp_add_func_16(){return 0;};
  namespace boost{namespace io{typedef int tmp_add_type_17;}}
  boost::io::tmp_add_type_17 tmp_add_func_17(){return 0;};
  namespace boost{namespace io{namespace detail{typedef int tmp_add_type_18;}}}
  boost::io::detail::tmp_add_type_18 tmp_add_func_18(){return 0;};
  namespace boost{namespace iostreams{typedef int tmp_add_type_19;}}
  boost::iostreams::tmp_add_type_19 tmp_add_func_19(){return 0;};
  namespace boost{namespace iostreams{namespace detail{typedef int tmp_add_type_20;}}}
  boost::iostreams::detail::tmp_add_type_20 tmp_add_func_20(){return 0;};
  namespace boost{namespace iterators{typedef int tmp_add_type_21;}}
  boost::iterators::tmp_add_type_21 tmp_add_func_21(){return 0;};
  namespace boost{namespace iterators{namespace detail{typedef int tmp_add_type_22;}}}
  boost::iterators::detail::tmp_add_type_22 tmp_add_func_22(){return 0;};
  namespace boost{namespace movelib{typedef int tmp_add_type_23;}}
  boost::movelib::tmp_add_type_23 tmp_add_func_23(){return 0;};
  namespace boost{namespace movelib{namespace detail{typedef int tmp_add_type_24;}}}
  boost::movelib::detail::tmp_add_type_24 tmp_add_func_24(){return 0;};
  namespace boost{namespace mpl{typedef int tmp_add_type_25;}}
  boost::mpl::tmp_add_type_25 tmp_add_func_25(){return 0;};
  namespace boost{namespace mpl{namespace aux{typedef int tmp_add_type_26;}}}
  boost::mpl::aux::tmp_add_type_26 tmp_add_func_26(){return 0;};
  namespace boost{namespace mpl{namespace placeholders{typedef int tmp_add_type_27;}}}
  boost::mpl::placeholders::tmp_add_type_27 tmp_add_func_27(){return 0;};
  namespace boost{namespace range{typedef int tmp_add_type_28;}}
  boost::range::tmp_add_type_28 tmp_add_func_28(){return 0;};
  namespace boost{namespace system{typedef int tmp_add_type_29;}}
  boost::system::tmp_add_type_29 tmp_add_func_29(){return 0;};
  namespace boost{namespace system{namespace detail{typedef int tmp_add_type_30;}}}
  boost::system::detail::tmp_add_type_30 tmp_add_func_30(){return 0;};
  namespace boost{namespace system{namespace errc{typedef int tmp_add_type_31;}}}
  boost::system::errc::tmp_add_type_31 tmp_add_func_31(){return 0;};
  namespace boost{namespace typeindex{typedef int tmp_add_type_32;}}
  boost::typeindex::tmp_add_type_32 tmp_add_func_32(){return 0;};
  namespace boost{namespace typeindex{namespace detail{typedef int tmp_add_type_33;}}}
  boost::typeindex::detail::tmp_add_type_33 tmp_add_func_33(){return 0;};
  namespace genome{typedef int tmp_add_type_34;}
  genome::tmp_add_type_34 tmp_add_func_34(){return 0;};
  namespace mems{typedef int tmp_add_type_35;}
  mems::tmp_add_type_35 tmp_add_func_35(){return 0;};
  namespace boost{namespace __anon135ff9dda611{typedef int tmp_add_type_36;}}
  boost::__anon135ff9dda611::tmp_add_type_36 tmp_add_func_36(){return 0;};
  namespace boost{namespace _mfi{typedef int tmp_add_type_37;}}
  boost::_mfi::tmp_add_type_37 tmp_add_func_37(){return 0;};
  namespace boost{namespace binary_op_detail{typedef int tmp_add_type_38;}}
  boost::binary_op_detail::tmp_add_type_38 tmp_add_func_38(){return 0;};
  namespace boost{namespace detail{namespace aligned_storage{typedef int tmp_add_type_39;}}}
  boost::detail::aligned_storage::tmp_add_type_39 tmp_add_func_39(){return 0;};
  namespace boost{namespace detail{namespace dynamic_bitset_impl{typedef int tmp_add_type_40;}}}
  boost::detail::dynamic_bitset_impl::tmp_add_type_40 tmp_add_func_40(){return 0;};
  namespace boost{namespace detail{namespace indirect_traits{typedef int tmp_add_type_41;}}}
  boost::detail::indirect_traits::tmp_add_type_41 tmp_add_func_41(){return 0;};
  namespace boost{namespace detail{namespace multi_array{typedef int tmp_add_type_42;}}}
  boost::detail::multi_array::tmp_add_type_42 tmp_add_func_42(){return 0;};
  namespace boost{namespace detail{namespace static_log2_impl{typedef int tmp_add_type_43;}}}
  boost::detail::static_log2_impl::tmp_add_type_43 tmp_add_func_43(){return 0;};
  namespace boost{namespace empty_{typedef int tmp_add_type_44;}}
  boost::empty_::tmp_add_type_44 tmp_add_func_44(){return 0;};
  namespace boost{namespace exception_detail{typedef int tmp_add_type_45;}}
  boost::exception_detail::tmp_add_type_45 tmp_add_func_45(){return 0;};
  namespace boost{namespace filesystem{namespace path_detail{typedef int tmp_add_type_46;}}}
  boost::filesystem::path_detail::tmp_add_type_46 tmp_add_func_46(){return 0;};
  namespace boost{namespace filesystem{namespace path_traits{typedef int tmp_add_type_47;}}}
  boost::filesystem::path_traits::tmp_add_type_47 tmp_add_func_47(){return 0;};
  namespace boost{namespace hash_detail{typedef int tmp_add_type_48;}}
  boost::hash_detail::tmp_add_type_48 tmp_add_func_48(){return 0;};
  namespace boost{namespace iostreams{namespace detail{namespace is_boost_stream_buffer_impl_{typedef int tmp_add_type_49;}}}}
  boost::iostreams::detail::is_boost_stream_buffer_impl_::tmp_add_type_49 tmp_add_func_49(){return 0;};
  namespace boost{namespace iostreams{namespace detail{namespace is_boost_stream_impl_{typedef int tmp_add_type_50;}}}}
  boost::iostreams::detail::is_boost_stream_impl_::tmp_add_type_50 tmp_add_func_50(){return 0;};
  namespace boost{namespace iostreams{namespace detail{namespace is_filtering_stream_impl_impl_{typedef int tmp_add_type_51;}}}}
  boost::iostreams::detail::is_filtering_stream_impl_impl_::tmp_add_type_51 tmp_add_func_51(){return 0;};
  namespace boost{namespace iostreams{namespace detail{namespace is_filtering_streambuf_impl_impl_{typedef int tmp_add_type_52;}}}}
  boost::iostreams::detail::is_filtering_streambuf_impl_impl_::tmp_add_type_52 tmp_add_func_52(){return 0;};
  namespace boost{namespace iostreams{namespace detail{namespace is_filtering_wstream_impl_impl_{typedef int tmp_add_type_53;}}}}
  boost::iostreams::detail::is_filtering_wstream_impl_impl_::tmp_add_type_53 tmp_add_func_53(){return 0;};
  namespace boost{namespace iostreams{namespace detail{namespace is_filtering_wstreambuf_impl_impl_{typedef int tmp_add_type_54;}}}}
  boost::iostreams::detail::is_filtering_wstreambuf_impl_impl_::tmp_add_type_54 tmp_add_func_54(){return 0;};
  namespace boost{namespace iostreams{namespace detail{namespace is_linked_impl_{typedef int tmp_add_type_55;}}}}
  boost::iostreams::detail::is_linked_impl_::tmp_add_type_55 tmp_add_func_55(){return 0;};
  namespace boost{namespace iostreams{namespace is_filebuf_impl_{typedef int tmp_add_type_56;}}}
  boost::iostreams::is_filebuf_impl_::tmp_add_type_56 tmp_add_func_56(){return 0;};
  namespace boost{namespace iostreams{namespace is_fstream_impl_{typedef int tmp_add_type_57;}}}
  boost::iostreams::is_fstream_impl_::tmp_add_type_57 tmp_add_func_57(){return 0;};
  namespace boost{namespace iostreams{namespace is_ifstream_impl_{typedef int tmp_add_type_58;}}}
  boost::iostreams::is_ifstream_impl_::tmp_add_type_58 tmp_add_func_58(){return 0;};
  namespace boost{namespace iostreams{namespace is_iostream_impl_{typedef int tmp_add_type_59;}}}
  boost::iostreams::is_iostream_impl_::tmp_add_type_59 tmp_add_func_59(){return 0;};
  namespace boost{namespace iostreams{namespace is_istream_impl_{typedef int tmp_add_type_60;}}}
  boost::iostreams::is_istream_impl_::tmp_add_type_60 tmp_add_func_60(){return 0;};
  namespace boost{namespace iostreams{namespace is_istringstream_impl_{typedef int tmp_add_type_61;}}}
  boost::iostreams::is_istringstream_impl_::tmp_add_type_61 tmp_add_func_61(){return 0;};
  namespace boost{namespace iostreams{namespace is_iterator_range_impl_{typedef int tmp_add_type_62;}}}
  boost::iostreams::is_iterator_range_impl_::tmp_add_type_62 tmp_add_func_62(){return 0;};
  namespace boost{namespace iostreams{namespace is_ofstream_impl_{typedef int tmp_add_type_63;}}}
  boost::iostreams::is_ofstream_impl_::tmp_add_type_63 tmp_add_func_63(){return 0;};
  namespace boost{namespace iostreams{namespace is_ostream_impl_{typedef int tmp_add_type_64;}}}
  boost::iostreams::is_ostream_impl_::tmp_add_type_64 tmp_add_func_64(){return 0;};
  namespace boost{namespace iostreams{namespace is_ostringstream_impl_{typedef int tmp_add_type_65;}}}
  boost::iostreams::is_ostringstream_impl_::tmp_add_type_65 tmp_add_func_65(){return 0;};
  namespace boost{namespace iostreams{namespace is_streambuf_impl_{typedef int tmp_add_type_66;}}}
  boost::iostreams::is_streambuf_impl_::tmp_add_type_66 tmp_add_func_66(){return 0;};
  namespace boost{namespace iostreams{namespace is_stringbuf_impl_{typedef int tmp_add_type_67;}}}
  boost::iostreams::is_stringbuf_impl_::tmp_add_type_67 tmp_add_func_67(){return 0;};
  namespace boost{namespace iostreams{namespace is_stringstream_impl_{typedef int tmp_add_type_68;}}}
  boost::iostreams::is_stringstream_impl_::tmp_add_type_68 tmp_add_func_68(){return 0;};
  namespace boost{namespace iterator_range_detail{typedef int tmp_add_type_69;}}
  boost::iterator_range_detail::tmp_add_type_69 tmp_add_func_69(){return 0;};
  namespace boost{namespace iterators{namespace advance_adl_barrier{typedef int tmp_add_type_70;}}}
  boost::iterators::advance_adl_barrier::tmp_add_type_70 tmp_add_func_70(){return 0;};
  namespace boost{namespace iterators{namespace distance_adl_barrier{typedef int tmp_add_type_71;}}}
  boost::iterators::distance_adl_barrier::tmp_add_type_71 tmp_add_func_71(){return 0;};
  namespace boost{namespace move_detail{typedef int tmp_add_type_72;}}
  boost::move_detail::tmp_add_type_72 tmp_add_func_72(){return 0;};
  namespace boost{namespace multi_array_concepts{typedef int tmp_add_type_73;}}
  boost::multi_array_concepts::tmp_add_type_73 tmp_add_func_73(){return 0;};
  namespace boost{namespace multi_array_concepts{namespace detail{typedef int tmp_add_type_74;}}}
  boost::multi_array_concepts::detail::tmp_add_type_74 tmp_add_func_74(){return 0;};
  namespace boost{namespace multi_array_types{typedef int tmp_add_type_75;}}
  boost::multi_array_types::tmp_add_type_75 tmp_add_func_75(){return 0;};
  namespace boost{namespace next_prior_detail{typedef int tmp_add_type_76;}}
  boost::next_prior_detail::tmp_add_type_76 tmp_add_func_76(){return 0;};
  namespace boost{namespace noncopyable_{typedef int tmp_add_type_77;}}
  boost::noncopyable_::tmp_add_type_77 tmp_add_func_77(){return 0;};
  namespace boost{namespace range_adl_barrier{typedef int tmp_add_type_78;}}
  boost::range_adl_barrier::tmp_add_type_78 tmp_add_func_78(){return 0;};
  namespace boost{namespace range_detail{typedef int tmp_add_type_79;}}
  boost::range_detail::tmp_add_type_79 tmp_add_func_79(){return 0;};
  namespace boost{namespace range_distance_adl_barrier{typedef int tmp_add_type_80;}}
  boost::range_distance_adl_barrier::tmp_add_type_80 tmp_add_func_80(){return 0;};
  namespace boost{namespace sp_adl_block{typedef int tmp_add_type_81;}}
  boost::sp_adl_block::tmp_add_type_81 tmp_add_func_81(){return 0;};
  namespace boost{namespace tt_align_ns{typedef int tmp_add_type_82;}}
  boost::tt_align_ns::tmp_add_type_82 tmp_add_func_82(){return 0;};
  namespace boost{namespace type_traits{typedef int tmp_add_type_83;}}
  boost::type_traits::tmp_add_type_83 tmp_add_func_83(){return 0;};
  namespace boost{namespace type_traits{namespace detail{typedef int tmp_add_type_84;}}}
  boost::type_traits::detail::tmp_add_type_84 tmp_add_func_84(){return 0;};
  namespace boost{namespace type_traits_detail{typedef int tmp_add_type_85;}}
  boost::type_traits_detail::tmp_add_type_85 tmp_add_func_85(){return 0;};
  namespace boost{namespace type_traits_swappable_detail{typedef int tmp_add_type_86;}}
  boost::type_traits_swappable_detail::tmp_add_type_86 tmp_add_func_86(){return 0;};
  namespace boost_concepts{typedef int tmp_add_type_87;}
  boost_concepts::tmp_add_type_87 tmp_add_func_87(){return 0;};
  namespace boost_concepts{namespace detail{typedef int tmp_add_type_88;}}
  boost_concepts::detail::tmp_add_type_88 tmp_add_func_88(){return 0;};
  namespace boost_swap_impl{typedef int tmp_add_type_89;}
  boost_swap_impl::tmp_add_type_89 tmp_add_func_89(){return 0;};
  namespace mpl_{typedef int tmp_add_type_90;}
  mpl_::tmp_add_type_90 tmp_add_func_90(){return 0;};
  namespace mpl_{namespace aux{typedef int tmp_add_type_91;}}
  mpl_::aux::tmp_add_type_91 tmp_add_func_91(){return 0;};

  // add classes
  BFloat* tmp_add_class_0;
  BFloatMethods* tmp_add_class_1;
  HomologyBaumWelch* tmp_add_class_2;
  HomologyDPTable* tmp_add_class_3;
  Logspace* tmp_add_class_4;
  LogspaceMethods* tmp_add_class_5;
  Params* tmp_add_class_6;
  Path* tmp_add_class_7;
  SMLHeader_s* tmp_add_class_8;
  SimplePath* tmp_add_class_9;
  TreeNode* tmp_add_class_10;
  _BFloatInitialize* tmp_add_class_11;
  _G_fpos64_t* tmp_add_class_12;
  _G_fpos_t* tmp_add_class_13;
  _IO_cookie_io_functions_t* tmp_add_class_14;
  _aFILE* tmp_add_class_15;
  _aIORec* tmp_add_class_16;
  bin_s* tmp_add_class_17;
  buffer_list_s* tmp_add_class_18;
  buffer_s* tmp_add_class_19;
  device_s* tmp_add_class_20;
  iodevice_s* tmp_add_class_21;
  record_s* tmp_add_class_22;
  seqbuf_s* tmp_add_class_23;
  sml_s* tmp_add_class_24;
  sort_buf_s* tmp_add_class_25;
  working_set_s* tmp_add_class_26;

The GCC parameters:
  gcc -fdump-lang-raw -fkeep-inline-functions -c -x c++ -fpermissive -w "/tmp/NyLyVFOGg0/dump1.h"

In file included from /tmp/NyLyVFOGg0/dump1.h:12:
/usr/include/libMems/AbstractGappedAlignment.h:80:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’?
   80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment );
      |                                                                        ^~~~~~~~~~
      |                                                                        gnContigSequence
/usr/include/libMems/AbstractGappedAlignment.h:80:84: error: template argument 1 is invalid
   80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment );
      |                                                                                    ^
/usr/include/libMems/AbstractGappedAlignment.h:80:84: error: template argument 2 is invalid
/usr/include/libMems/AbstractGappedAlignment.h:80:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’?
   80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment );
      |                                                                        ^~~~~~~~~~
      |                                                                        gnContigSequence
/usr/include/libMems/AbstractGappedAlignment.h:80:84: error: template argument 1 is invalid
   80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment );
      |                                                                                    ^
/usr/include/libMems/AbstractGappedAlignment.h:80:84: error: template argument 2 is invalid
/usr/include/libMems/AbstractGappedAlignment.h:80:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’?
   80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment );
      |                                                                        ^~~~~~~~~~
      |                                                                        gnContigSequence
/usr/include/libMems/AbstractGappedAlignment.h:80:84: error: template argument 1 is invalid
   80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment );
      |                                                                                    ^
/usr/include/libMems/AbstractGappedAlignment.h:80:84: error: template argument 2 is invalid
/usr/include/libMems/AbstractGappedAlignment.h:80:51: error: invalid template-id
   80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment );
      |                                                   ^~~
/usr/include/libMems/AbstractGappedAlignment.h:80:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’?
   80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment );
      |                                                                        ^~~~~~~~~~
      |                                                                        gnContigSequence
/usr/include/libMems/AbstractGappedAlignment.h:80:84: error: expected primary-expression before ‘>’ token
   80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment );
      |                                                                                    ^
/usr/include/libMems/AbstractGappedAlignment.h:80:45: error: template placeholder type ‘const vector<...auto...>’ must be followed by a simple declarator-id
   80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment );
      |                                             ^~~~~
In file included from /usr/include/c++/12/vector:64,
                 from /usr/include/libMems/AbstractMatch.h:17,
                 from /usr/include/libMems/AbstractGappedAlignment.h:16:
/usr/include/c++/12/bits/stl_vector.h:423:11: note: ‘template<class _Tp, class _Alloc> class std::vector’ declared here
  423 |     class vector : protected _Vector_base<_Tp, _Alloc>
      |           ^~~~~~
/usr/include/libMems/AbstractGappedAlignment.h:80:96: error: expected ‘)’ before ‘,’ token
   80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment );
      |                  ~                                                                             ^
      |                                                                                                )
/usr/include/libMems/AbstractGappedAlignment.h:80:122: error: invalid declarator before ‘&’ token
   80 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment );
      |                                                                                                                          ^
/usr/include/libMems/AbstractGappedAlignment.h:84:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’?
   84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment )
      |                                                                        ^~~~~~~~~~
      |                                                                        gnContigSequence
/usr/include/libMems/AbstractGappedAlignment.h:84:84: error: template argument 1 is invalid
   84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment )
      |                                                                                    ^
/usr/include/libMems/AbstractGappedAlignment.h:84:84: error: template argument 2 is invalid
/usr/include/libMems/AbstractGappedAlignment.h:84:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’?
   84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment )
      |                                                                        ^~~~~~~~~~
      |                                                                        gnContigSequence
/usr/include/libMems/AbstractGappedAlignment.h:84:84: error: template argument 1 is invalid
   84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment )
      |                                                                                    ^
/usr/include/libMems/AbstractGappedAlignment.h:84:84: error: template argument 2 is invalid
/usr/include/libMems/AbstractGappedAlignment.h:84:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’?
   84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment )
      |                                                                        ^~~~~~~~~~
      |                                                                        gnContigSequence
/usr/include/libMems/AbstractGappedAlignment.h:84:84: error: template argument 1 is invalid
   84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment )
      |                                                                                    ^
/usr/include/libMems/AbstractGappedAlignment.h:84:84: error: template argument 2 is invalid
/usr/include/libMems/AbstractGappedAlignment.h:84:51: error: invalid template-id
   84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment )
      |                                                   ^~~
/usr/include/libMems/AbstractGappedAlignment.h:84:72: error: ‘gnSequence’ is not a member of ‘genome’; did you mean ‘gnContigSequence’?
   84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment )
      |                                                                        ^~~~~~~~~~
      |                                                                        gnContigSequence
/usr/include/libMems/AbstractGappedAlignment.h:84:84: error: expected primary-expression before ‘>’ token
   84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment )
      |                                                                                    ^
/usr/include/libMems/AbstractGappedAlignment.h:84:45: error: template placeholder type ‘const vector<...auto...>’ must be followed by a simple declarator-id
   84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment )
      |                                             ^~~~~
/usr/include/c++/12/bits/stl_vector.h:423:11: note: ‘template<class _Tp, class _Alloc> class std::vector’ declared here
  423 |     class vector : protected _Vector_base<_Tp, _Alloc>
      |           ^~~~~~
/usr/include/libMems/AbstractGappedAlignment.h:84:96: error: expected ‘)’ before ‘,’ token
   84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment )
      |                  ~                                                                             ^
      |                                                                                                )
/usr/include/libMems/AbstractGappedAlignment.h:84:122: error: invalid declarator before ‘&’ token
   84 | void GetAlignment( const AbstractMatch& ga, const std::vector< genome::gnSequence* >& seq_table, std::vector<std::string>& alignment )
      |                                                                                                                          ^
In file included from /tmp/NyLyVFOGg0/dump1.h:20:
/usr/include/libMems/DistanceMatrix.h: In instantiation of ‘void mems::AddToMatchIdentityMatrix(const AbstractMatchType&, const std::vector<genome::gnSequence*>&, NumericMatrix<double>&) [with AbstractMatchType = AbstractMatch]’:
/usr/include/libMems/DistanceMatrix.h:60:27:   required from ‘void mems::IdentityMatrix(const AbstractMatchVectorType&, const std::vector<genome::gnSequence*>&, NumericMatrix<double>&) [with AbstractMatchVectorType = std::vector<const AbstractMatch*>]’
/usr/include/libMems/DistanceMatrix.h:45:16:   required from here
/usr/include/libMems/DistanceMatrix.h:164:21: error: cannot allocate an object of abstract type ‘mems::AbstractMatch’
  164 |         GetAlignment( amt, seq_table, alignment );
      |         ~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/include/libMems/AbstractMatch.h:88:7: note:   because the following virtual functions are pure within ‘mems::AbstractMatch’:
   88 | class AbstractMatch : public genome::gnClone {
      |       ^~~~~~~~~~~~~
In file included from /usr/include/libMems/AbstractMatch.h:16:
/usr/include/libGenome/gnClone.h:28:34: note:     ‘virtual genome::gnClone* genome::gnClone::Clone() const’
   28 |                 virtual gnClone* Clone() const = 0;
      |                                  ^~~~~
/usr/include/libMems/AbstractMatch.h:98:32: note:     ‘virtual mems::AbstractMatch* mems::AbstractMatch::Copy() const’
   98 |         virtual AbstractMatch* Copy() const = 0;
      |                                ^~~~
/usr/include/libMems/AbstractMatch.h:101:22: note:     ‘virtual void mems::AbstractMatch::Free()’
  101 |         virtual void Free() = 0;
      |                      ^~~~
/usr/include/libMems/AbstractMatch.h:104:24: note:     ‘virtual gnSeqI mems::AbstractMatch::Length(uint) const’
  104 |         virtual gnSeqI Length( uint seqI ) const = 0;
      |                        ^~~~~~
/usr/include/libMems/AbstractMatch.h:107:22: note:     ‘virtual void mems::AbstractMatch::SetLength(gnSeqI, uint)’
  107 |         virtual void SetLength( gnSeqI len, uint seqI ) = 0;
      |                      ^~~~~~~~~
/usr/include/libMems/AbstractMatch.h:111:23: note:     ‘virtual int64 mems::AbstractMatch::Start(uint) const’
  111 |         virtual int64 Start(uint startI) const = 0;
      |                       ^~~~~
/usr/include/libMems/AbstractMatch.h:115:22: note:     ‘virtual void mems::AbstractMatch::SetStart(uint, int64)’
  115 |         virtual void SetStart(uint seqI, int64 start) = 0;
      |                      ^~~~~~~~
/usr/include/libMems/AbstractMatch.h:126:24: note:     ‘virtual gnSeqI mems::AbstractMatch::LeftEnd(uint) const’
  126 |         virtual gnSeqI LeftEnd(uint seqI) const = 0;
      |                        ^~~~~~~
/usr/include/libMems/AbstractMatch.h:135:29: note:     ‘virtual mems::AbstractMatch::orientation mems::AbstractMatch::Orientation(uint) const’
  135 |         virtual orientation Orientation(uint seqI) const = 0;
      |                             ^~~~~~~~~~~
/usr/include/libMems/AbstractMatch.h:138:22: note:     ‘virtual void mems::AbstractMatch::SetLeftEnd(uint, gnSeqI)’
  138 |         virtual void SetLeftEnd(uint seqI, gnSeqI start) = 0;
      |                      ^~~~~~~~~~
/usr/include/libMems/AbstractMatch.h:141:22: note:     ‘virtual void mems::AbstractMatch::SetOrientation(uint, orientation)’
  141 |         virtual void SetOrientation(uint seqI, orientation o) = 0;
      |                      ^~~~~~~~~~~~~~
/usr/include/libMems/AbstractMatch.h:144:22: note:     ‘virtual void mems::AbstractMatch::MoveStart(int64)’
  144 |         virtual void MoveStart(int64 move_amount) = 0;
      |                      ^~~~~~~~~
/usr/include/libMems/AbstractMatch.h:146:22: note:     ‘virtual void mems::AbstractMatch::MoveEnd(int64)’
  146 |         virtual void MoveEnd(int64 move_amount) = 0;
      |                      ^~~~~~~
/usr/include/libMems/AbstractMatch.h:149:22: note:     ‘virtual uint mems::AbstractMatch::Multiplicity() const’
  149 |         virtual uint Multiplicity() const = 0;
      |                      ^~~~~~~~~~~~
/usr/include/libMems/AbstractMatch.h:152:22: note:     ‘virtual uint mems::AbstractMatch::SeqCount() const’
  152 |         virtual uint SeqCount() const = 0;
      |                      ^~~~~~~~
/usr/include/libMems/AbstractMatch.h:155:22: note:     ‘virtual uint mems::AbstractMatch::FirstStart() const’
  155 |         virtual uint FirstStart() const = 0;
      |                      ^~~~~~~~~~
/usr/include/libMems/AbstractMatch.h:158:24: note:     ‘virtual gnSeqI mems::AbstractMatch::AlignmentLength() const’
  158 |         virtual gnSeqI AlignmentLength() const = 0;
      |                        ^~~~~~~~~~~~~~~
/usr/include/libMems/AbstractMatch.h:161:22: note:     ‘virtual void mems::AbstractMatch::Invert()’
  161 |         virtual void Invert() = 0;
      |                      ^~~~~~
/usr/include/libMems/AbstractMatch.h:168:22: note:     ‘virtual void mems::AbstractMatch::CropStart(gnSeqI)’
  168 |         virtual void CropStart(gnSeqI crop_amount) = 0;
      |                      ^~~~~~~~~
/usr/include/libMems/AbstractMatch.h:173:22: note:     ‘virtual void mems::AbstractMatch::CropEnd(gnSeqI)’
  173 |         virtual void CropEnd(gnSeqI crop_amount) = 0;
      |                      ^~~~~~~
/usr/include/libMems/AbstractMatch.h:179:22: note:     ‘virtual void mems::AbstractMatch::CropLeft(gnSeqI, uint)’
  179 |         virtual void CropLeft(gnSeqI crop_amount, uint seqI) = 0;
      |                      ^~~~~~~~
/usr/include/libMems/AbstractMatch.h:184:22: note:     ‘virtual void mems::AbstractMatch::CropRight(gnSeqI, uint)’
  184 |         virtual void CropRight(gnSeqI crop_amount, uint seqI) = 0;
      |                      ^~~~~~~~~
/usr/include/libMems/AbstractMatch.h:191:22: note:     ‘virtual void mems::AbstractMatch::GetAlignment(std::vector<boost::dynamic_bitset<> >&) const’
  191 |         virtual void GetAlignment( std::vector< bitset_t >& align_matrix ) const = 0;
      |                      ^~~~~~~~~~~~
/usr/include/libMems/AbstractMatch.h:200:22: note:     ‘virtual void mems::AbstractMatch::GetColumn(gnSeqI, std::vector<long long unsigned int>&, std::vector<bool>&) const’
  200 |         virtual void GetColumn( gnSeqI col, std::vector<gnSeqI>& pos, std::vector<bool>& column ) const = 0;
      |                      ^~~~~~~~~
/usr/include/libMems/AbstractMatch.h:204:22: note:     ‘virtual bool mems::AbstractMatch::IsGap(uint, gnSeqI) const’
  204 |         virtual bool IsGap( uint seq, gnSeqI col ) const = 0;
      |                      ^~~~~
/usr/include/libMems/AbstractMatch.h:206:22: note:     ‘virtual uint mems::AbstractMatch::UsedSeq(uint) const’
  206 |         virtual uint UsedSeq( uint seqI ) const = 0;
      |                      ^~~~~~~

