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CMake 0.03% Shell 0.35% C 0.25% C++ 94.88% Objective-C 2.90% CSS 0.14% JavaScript 0.28% Python 1.18%

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triplexator's Issues

Number of tpx reported in output and summary does not correspond

Dear authors,
I find discrepancies in the number of TPX reported in the output file and in the summary file, e.g. summary report 27 Total TPX while there are 17 rows in the output file. The number of TPX reported in the summary file (used to calculate the triplex potential) is always bigger than the number of rows reported in output.

The command line I used:

$ triplexator -l 10 -L -1 -e 20 -E -1 -fm 1 -of 1 -o -rm 2 -p 10 -ss ssRNA.fa -ds dsDNA.da

dsDNA.da contain

GGAAGGAGCTGTGCATTGAGGGGTGAAAGCCCGTGCAGAGAACCGTGGGAGAAAGAGGCTGTGGACACGGGGCGGAAGAG
AGGGCTGGGGCGCAGTCGTCAGCTGCCGTGACCCCACAGCTGGGAGCAAGCTGATTCCTGCCTCGGAGCTGCCGTCTCCC
CTGCTGGCCGTTCTCTCTCCCGTGGGGAAACGCCCCCCCCCCCCCCCCGCCCTGCACCTGGCTGGCGGCACCTGTGGGCA
CTGACCACTCCACGCCAGCTGTTTTCCTTGGTTGGGGTTGGGGGCACCGAGCGTTTGGGTGGACCGGAAGTCAGCGTCTG
CATTCGAGCCTGTGTGCGGTGCATGGGCCAAGGGCGCCCACACCCACGCCACCCTTTCCGAAGGAACCGAGCCCCAGCCC
CTCATGG

ssRNA.fa contain

>TERC
GGGTTGCGGAGGGTGGGCCTGGGAGGGGTGGTGGCCATTTTTTGTCTAACCCTAACTGAGAAGGGCGTAGGCGCCGTGCT
TTTGCTCCCCGCGCGCTGTTTTTCTCGCTGACTTTCAGCGGGCGGAAAAGCCTCGGCCTGCCGCCTTCCACCGTTCATTC
TAGAGCAAACAAAAAATGTCAGCTGCTGGCCCGTTCGCCCCTCCCGGGGACCTGCGGCGGGTCGCCTGCCCAGCCCCCGA
ACCCCGCCTGGAGGCCGCGGTCGGCCCGGGGCTTCTCCGGAGGCACCCACTGCCACCGCGAAGAGTTGGGCTCTGTCAGC
CGCGGGTCTCTCGGGGGCGAGGGCGAGGTTCAGGCCTTTCAGGCCGCAGGAAGAGGAACGGAGCGAGTCCCCGCGCGCGG
CGCGATTCCCTGAGCTGTGGGACGTGCACCCAGGACTCGGCTCACACATGCAGTTCGCTTTCCTGTTGGTGGGGGGAACG
CCGATCGTGCGCATCCGTCACCCCTCGCCGGCAATGGGGGCTTGTGAACCCCCAAACCTGA

MacOS high sierra doesn't support gcc47 compiler

Hi,

I have a problem with installing triplexator on macOS 10.13 because the gcc47 compiler has been deprecated in newer OS versions. I get the following error:

dyld: Library not loaded: /opt/local/lib/gcc47/libgomp.1.dylib
Referenced from: /Users/xyz/tools/triplexator-1.3.2-Darwin/bin/triplexator
Reason: image not found

Issue with cmake compilation

** @Gurado Please, help resolve this issue with compiling triplexator:-**

> cmake ../.. -DCMAKE_BUILD_TYPE=Release -DCMAKE_CXX_COMPILER=g++ -G "Unix Makefiles" && make

-- Boost version: 1.65.1
-- Found the following Boost libraries:
--   iostreams
--   regex
CMake Warning (dev) at /usr/share/cmake-3.10/Modules/FindOpenMP.cmake:310 (if):
  if given arguments:

    "TRUE"

  An argument named "TRUE" appears in a conditional statement.  Policy
  CMP0012 is not set: if() recognizes numbers and boolean constants.  Run
  "cmake --help-policy CMP0012" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/FindOpenMP.cmake:425 (_OPENMP_GET_SPEC_DATE)
  CMakeLists.txt:13 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at /usr/share/cmake-3.10/Modules/FindOpenMP.cmake:310 (if):
  if given arguments:

    "TRUE"

  An argument named "TRUE" appears in a conditional statement.  Policy
  CMP0012 is not set: if() recognizes numbers and boolean constants.  Run
  "cmake --help-policy CMP0012" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.
Call Stack (most recent call first):
  /usr/share/cmake-3.10/Modules/FindOpenMP.cmake:425 (_OPENMP_GET_SPEC_DATE)
  CMakeLists.txt:13 (find_package)
This warning is for project developers.  Use -Wno-dev to suppress it.

CMake Warning (dev) at src/CMakeLists.txt:3 (project):
  Policy CMP0048 is not set: project() command manages VERSION variables.
  Run "cmake --help-policy CMP0048" for policy details.  Use the cmake_policy
  command to set the policy and suppress this warning.

  The following variable(s) would be set to empty:

    triplexator_VERSION_MAJOR
    triplexator_VERSION_MINOR
    triplexator_VERSION_PATCH
This warning is for project developers.  Use -Wno-dev to suppress it.

Boost_IOSTREAMS_LIBRARY_RELEASE = /usr/lib/x86_64-linux-gnu/libboost_iostreams.so
-- Configuring done
-- Generating done
-- Build files have been written to: /home/josoga2/triplexator/build/Release
[ 50%] Building CXX object src/CMakeFiles/triplexator.dir/triplexator.cpp.o
In file included from /home/josoga2/triplexator/src/seqan/file.h:60:0,
                 from /home/josoga2/triplexator/src/seqan/misc/cmdparser/cmdparser.h:39,
                 from /home/josoga2/triplexator/src/seqan/misc/misc_cmdparser.h:36,
                 from /home/josoga2/triplexator/src/triplexator.cpp:54:
/home/josoga2/triplexator/src/seqan/file/file_generated_forwards.h:933:66: error: invalid abstract return type ‘seqan::FileFormat<TFile, TData, TMeta, void>’
 template <typename TFile, typename TData, typename TMeta> inline FileFormat<TFile, TData, TMeta, void> guessFileFormat(TFile & file, TData & data);        // "/Users/fabianbuske/Documents/research/triplex/seqan/core/include/seqan/file/file_format_guess.h"(77)
                                                                  ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/josoga2/triplexator/src/seqan/file.h:93:0,
                 from /home/josoga2/triplexator/src/seqan/misc/cmdparser/cmdparser.h:39,
                 from /home/josoga2/triplexator/src/seqan/misc/misc_cmdparser.h:36,
                 from /home/josoga2/triplexator/src/triplexator.cpp:54:
/home/josoga2/triplexator/src/seqan/file/file_format.h:197:8: note:   because the following virtual functions are pure within ‘seqan::FileFormat<TFile, TData, TMeta, void>’:
 struct FileFormat<TFile, TData, TMeta, void>
        ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/home/josoga2/triplexator/src/seqan/file/file_format.h:209:2: note: 	virtual void* seqan::FileFormat<TFile, TData, TMeta, void>::formatID_() const
  formatID_() const = 0;
  ^~~~~~~~~
/home/josoga2/triplexator/src/seqan/file/file_format.h:212:2: note: 	virtual void seqan::FileFormat<TFile, TData, TMeta, void>::read_(TFile&, TData&) const
  read_(TFile & file, TData & data) const = 0;
  ^~~~~
/home/josoga2/triplexator/src/seqan/file/file_format.h:214:2: note: 	virtual void seqan::FileFormat<TFile, TData, TMeta, void>::read_(TFile&, TData&, seqan::FileFormat<TFile, TData, TMeta, void>::TSize) const
  read_(TFile & file, TData & data, TSize limit) const = 0;
  ^~~~~
/home/josoga2/triplexator/src/seqan/file/file_format.h:217:2: note: 	virtual void seqan::FileFormat<TFile, TData, TMeta, void>::readMeta_(TFile&, TMeta&) const
  readMeta_(TFile & file, TMeta & meta) const = 0;
  ^~~~~~~~~
/home/josoga2/triplexator/src/seqan/file/file_format.h:220:2: note: 	virtual void seqan::FileFormat<TFile, TData, TMeta, void>::goNext_(TFile&) const
  goNext_(TFile & file) const = 0;
  ^~~~~~~
/home/josoga2/triplexator/src/seqan/file/file_format.h:223:2: note: 	virtual seqan::FileFormat<TFile, TData, TMeta, void>::TSize seqan::FileFormat<TFile, TData, TMeta, void>::length_(TFile&) const
  length_(TFile & file) const = 0;
  ^~~~~~~
/home/josoga2/triplexator/src/seqan/file/file_format.h:226:2: note: 	virtual void seqan::FileFormat<TFile, TData, TMeta, void>::write_(TFile&, TData&) const
  write_(TFile & file, TData & data) const = 0;
  ^~~~~~
/home/josoga2/triplexator/src/seqan/file/file_format.h:228:2: note: 	virtual void seqan::FileFormat<TFile, TData, TMeta, void>::write_(TFile&, TData&, TMeta&) const
  write_(TFile & file, TData & data, TMeta & meta) const = 0;
  ^~~~~~
/home/josoga2/triplexator/src/triplexator.cpp: In instantiation of ‘void seqan::_investigateTTSconsecutively(TDuplexName, TInput&, TSeqNo&, TMap&, TString&, TOutput&, seqan::Options&) [with TDuplexName = std::__cxx11::basic_string<char>; TInput = std::basic_ifstream<char>; TSeqNo = unsigned int; TMap = std::map<unsigned int, std::pair<std::__cxx11::basic_string<char>, unsigned int> >; TString = seqan::StringSet<seqan::String<char, seqan::Alloc<void> > >; TOutput = std::basic_ofstream<char>]’:
/home/josoga2/triplexator/src/triplexator.cpp:1179:32:   required from ‘void seqan::_investigateTTS(TDuplexName, TInput&, TSeqNo&, TMap&, TString&, TOutput&, seqan::Options&) [with TDuplexName = std::__cxx11::basic_string<char>; TInput = std::basic_ifstream<char>; TSeqNo = unsigned int; TMap = std::map<unsigned int, std::pair<std::__cxx11::basic_string<char>, unsigned int> >; TString = seqan::StringSet<seqan::String<char, seqan::Alloc<void> > >; TOutput = std::basic_ofstream<char>]’
/home/josoga2/triplexator/src/triplexator.cpp:1241:20:   required from ‘int seqan::investigateTTS(seqan::Options&) [with TTargetSet = seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >]’
/home/josoga2/triplexator/src/triplexator.cpp:1418:47:   required from here
/home/josoga2/triplexator/src/triplexator.cpp:920:138: error: no matching function for call to ‘make_pair<std::__cxx11::string, unsigned int>(std::__cxx11::basic_string<char>&, unsigned int&)’
 ::string,unsigned> >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile)));
                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/7/bits/char_traits.h:39,
                 from /usr/include/c++/7/ios:40,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/sstream:38,
                 from /home/josoga2/triplexator/src/seqan/misc/cmdparser/cmdparser.h:36,
                 from /home/josoga2/triplexator/src/seqan/misc/misc_cmdparser.h:36,
                 from /home/josoga2/triplexator/src/triplexator.cpp:54:
/usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
     make_pair(_T1&& __x, _T2&& __y)
     ^~~~~~~~~
/usr/include/c++/7/bits/stl_pair.h:524:5: note:   template argument deduction/substitution failed:
/home/josoga2/triplexator/src/triplexator.cpp:920:138: note:   cannot convert ‘filename’ (type ‘std::__cxx11::basic_string<char>’) to type ‘std::__cxx11::basic_string<char>&&’
 ::string,unsigned> >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile)));
                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/home/josoga2/triplexator/src/triplexator.cpp: In instantiation of ‘void seqan::_investigateTTSsimultaneous(TDuplexName, TInput&, TSeqNo&, TMap&, TString&, TOutput&, seqan::Options&) [with TDuplexName = std::__cxx11::basic_string<char>; TInput = std::basic_ifstream<char>; TSeqNo = unsigned int; TMap = std::map<unsigned int, std::pair<std::__cxx11::basic_string<char>, unsigned int> >; TString = seqan::StringSet<seqan::String<char, seqan::Alloc<void> > >; TOutput = std::basic_ofstream<char>]’:
/home/josoga2/triplexator/src/triplexator.cpp:1181:31:   required from ‘void seqan::_investigateTTS(TDuplexName, TInput&, TSeqNo&, TMap&, TString&, TOutput&, seqan::Options&) [with TDuplexName = std::__cxx11::basic_string<char>; TInput = std::basic_ifstream<char>; TSeqNo = unsigned int; TMap = std::map<unsigned int, std::pair<std::__cxx11::basic_string<char>, unsigned int> >; TString = seqan::StringSet<seqan::String<char, seqan::Alloc<void> > >; TOutput = std::basic_ofstream<char>]’
/home/josoga2/triplexator/src/triplexator.cpp:1241:20:   required from ‘int seqan::investigateTTS(seqan::Options&) [with TTargetSet = seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >]’
/home/josoga2/triplexator/src/triplexator.cpp:1418:47:   required from here
/home/josoga2/triplexator/src/triplexator.cpp:1043:138: error: no matching function for call to ‘make_pair<std::__cxx11::string, unsigned int>(std::__cxx11::basic_string<char>&, unsigned int&)’
 ::string,unsigned> >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile)));
                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/7/bits/char_traits.h:39,
                 from /usr/include/c++/7/ios:40,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/sstream:38,
                 from /home/josoga2/triplexator/src/seqan/misc/cmdparser/cmdparser.h:36,
                 from /home/josoga2/triplexator/src/seqan/misc/misc_cmdparser.h:36,
                 from /home/josoga2/triplexator/src/triplexator.cpp:54:
/usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
     make_pair(_T1&& __x, _T2&& __y)
     ^~~~~~~~~
/usr/include/c++/7/bits/stl_pair.h:524:5: note:   template argument deduction/substitution failed:
/home/josoga2/triplexator/src/triplexator.cpp:1043:138: note:   cannot convert ‘filename’ (type ‘std::__cxx11::basic_string<char>’) to type ‘std::__cxx11::basic_string<char>&&’
 ::string,unsigned> >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile)));
                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/home/josoga2/triplexator/src/triplexator.cpp: In instantiation of ‘void seqan::_investigateTTSconsecutively(TDuplexName, TInput&, TSeqNo&, TMap&, TString&, TOutput&, seqan::Options&) [with TDuplexName = std::__cxx11::basic_string<char>; TInput = std::basic_ifstream<char>; TSeqNo = unsigned int; TMap = std::map<unsigned int, std::pair<std::__cxx11::basic_string<char>, unsigned int> >; TString = seqan::StringSet<seqan::String<char, seqan::Alloc<void> > >; TOutput = std::basic_ostream<char>]’:
/home/josoga2/triplexator/src/triplexator.cpp:1179:32:   required from ‘void seqan::_investigateTTS(TDuplexName, TInput&, TSeqNo&, TMap&, TString&, TOutput&, seqan::Options&) [with TDuplexName = std::__cxx11::basic_string<char>; TInput = std::basic_ifstream<char>; TSeqNo = unsigned int; TMap = std::map<unsigned int, std::pair<std::__cxx11::basic_string<char>, unsigned int> >; TString = seqan::StringSet<seqan::String<char, seqan::Alloc<void> > >; TOutput = std::basic_ostream<char>]’
/home/josoga2/triplexator/src/triplexator.cpp:1245:20:   required from ‘int seqan::investigateTTS(seqan::Options&) [with TTargetSet = seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >]’
/home/josoga2/triplexator/src/triplexator.cpp:1418:47:   required from here
/home/josoga2/triplexator/src/triplexator.cpp:920:138: error: no matching function for call to ‘make_pair<std::__cxx11::string, unsigned int>(std::__cxx11::basic_string<char>&, unsigned int&)’
 ::string,unsigned> >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile)));
                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/7/bits/char_traits.h:39,
                 from /usr/include/c++/7/ios:40,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/sstream:38,
                 from /home/josoga2/triplexator/src/seqan/misc/cmdparser/cmdparser.h:36,
                 from /home/josoga2/triplexator/src/seqan/misc/misc_cmdparser.h:36,
                 from /home/josoga2/triplexator/src/triplexator.cpp:54:
/usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
     make_pair(_T1&& __x, _T2&& __y)
     ^~~~~~~~~
/usr/include/c++/7/bits/stl_pair.h:524:5: note:   template argument deduction/substitution failed:
/home/josoga2/triplexator/src/triplexator.cpp:920:138: note:   cannot convert ‘filename’ (type ‘std::__cxx11::basic_string<char>’) to type ‘std::__cxx11::basic_string<char>&&’
 ::string,unsigned> >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile)));
                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
/home/josoga2/triplexator/src/triplexator.cpp: In instantiation of ‘void seqan::_investigateTTSsimultaneous(TDuplexName, TInput&, TSeqNo&, TMap&, TString&, TOutput&, seqan::Options&) [with TDuplexName = std::__cxx11::basic_string<char>; TInput = std::basic_ifstream<char>; TSeqNo = unsigned int; TMap = std::map<unsigned int, std::pair<std::__cxx11::basic_string<char>, unsigned int> >; TString = seqan::StringSet<seqan::String<char, seqan::Alloc<void> > >; TOutput = std::basic_ostream<char>]’:
/home/josoga2/triplexator/src/triplexator.cpp:1181:31:   required from ‘void seqan::_investigateTTS(TDuplexName, TInput&, TSeqNo&, TMap&, TString&, TOutput&, seqan::Options&) [with TDuplexName = std::__cxx11::basic_string<char>; TInput = std::basic_ifstream<char>; TSeqNo = unsigned int; TMap = std::map<unsigned int, std::pair<std::__cxx11::basic_string<char>, unsigned int> >; TString = seqan::StringSet<seqan::String<char, seqan::Alloc<void> > >; TOutput = std::basic_ostream<char>]’
/home/josoga2/triplexator/src/triplexator.cpp:1245:20:   required from ‘int seqan::investigateTTS(seqan::Options&) [with TTargetSet = seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >]’
/home/josoga2/triplexator/src/triplexator.cpp:1418:47:   required from here
/home/josoga2/triplexator/src/triplexator.cpp:1043:138: error: no matching function for call to ‘make_pair<std::__cxx11::string, unsigned int>(std::__cxx11::basic_string<char>&, unsigned int&)’
 ::string,unsigned> >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile)));
                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /usr/include/c++/7/bits/stl_algobase.h:64:0,
                 from /usr/include/c++/7/bits/char_traits.h:39,
                 from /usr/include/c++/7/ios:40,
                 from /usr/include/c++/7/istream:38,
                 from /usr/include/c++/7/sstream:38,
                 from /home/josoga2/triplexator/src/seqan/misc/cmdparser/cmdparser.h:36,
                 from /home/josoga2/triplexator/src/seqan/misc/misc_cmdparser.h:36,
                 from /home/josoga2/triplexator/src/triplexator.cpp:54:
/usr/include/c++/7/bits/stl_pair.h:524:5: note: candidate: template<class _T1, class _T2> constexpr std::pair<typename std::__decay_and_strip<_Tp>::__type, typename std::__decay_and_strip<_T2>::__type> std::make_pair(_T1&&, _T2&&)
     make_pair(_T1&& __x, _T2&& __y)
     ^~~~~~~~~
/usr/include/c++/7/bits/stl_pair.h:524:5: note:   template argument deduction/substitution failed:
/home/josoga2/triplexator/src/triplexator.cpp:1043:138: note:   cannot convert ‘filename’ (type ‘std::__cxx11::basic_string<char>’) to type ‘std::__cxx11::basic_string<char>&&’
 ::string,unsigned> >(seqNo,::std::make_pair< ::std::string,unsigned>(filename,seqNoWithinFile)));
                            ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~~~~~~~~~~~~~~~~~~~~~~~~
In file included from /home/josoga2/triplexator/src/gardener.h:39:0,
                 from /home/josoga2/triplexator/src/triplex.h:50,
                 from /home/josoga2/triplexator/src/triplexator.h:44,
                 from /home/josoga2/triplexator/src/triplexator.cpp:57:
/home/josoga2/triplexator/src/find_index_qgrams.h: In instantiation of ‘bool seqan::_seedMultiProcessQGram(TFinder&, const seqan::Pattern<TIndex, seqan::QGramsLookup<TSpec> >&, THashValue) [with TFinder = seqan::Finder<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > >, seqan::QGramsLookup<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >, const seqan::Tag<seqan::Finder_QGramsLookup_> > >; TIndex = seqan::Index<seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >, seqan::Tag<seqan::OpenAddressing_> > >; THashValue = long unsigned int; TSpec = seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >]’:
/home/josoga2/triplexator/src/find_index_qgrams.h:349:30:   required from ‘bool seqan::find(seqan::Finder<THaystack, seqan::QGramsLookup<TShape, TSpec> >&, const seqan::Pattern<TIndex, seqan::QGramsLookup<TShape, TSpec> >&) [with THaystack = seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > >; TIndex = seqan::Index<seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >, seqan::Tag<seqan::OpenAddressing_> > >; TShape = seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >; TSpec = const seqan::Tag<seqan::Finder_QGramsLookup_>]’
/home/josoga2/triplexator/src/gardener.h:993:14:   required from ‘void seqan::_collectSeeds(seqan::Finder<THaystack, seqan::QGramsLookup<TSpec> >&, const seqan::Pattern<TIndex, seqan::QGramsLookup<TSpec> >&, const TPos&, const TPos&, TMap&) [with THaystack = seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > >; TSpec = seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >; TIndex = seqan::Index<seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >, seqan::Tag<seqan::OpenAddressing_> > >; TPos = unsigned int; TMap = seqan::Map<seqan::Pair<long int, seqan::Map<seqan::Pair<int, seqan::Dequeue<seqan::Seed<seqan::Tag<seqan::Simple_>, seqan::DefaultSeedConfig> >*, void>, seqan::Skiplist<> >*, void>, seqan::Skiplist<> >]’
/home/josoga2/triplexator/src/gardener.h:1115:17:   required from ‘bool seqan::_find(THitSet&, seqan::Finder<THaystack, TSpec>&, const seqan::Pattern<TIndex, TSpec>&, const TError&, const TPos&, const TPos&, const TDrop&, TId&) [with THitSet = seqan::Map<seqan::GardenerHit_<seqan::Tag<seqan::GardenerUngapped_>, long int, long int>, seqan::Skiplist<> >; THaystack = seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > >; TSpec = seqan::QGramsLookup<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >, const seqan::Tag<seqan::Finder_QGramsLookup_> >; TIndex = seqan::Index<seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >, seqan::Tag<seqan::OpenAddressing_> > >; TError = double; TPos = unsigned int; TDrop = unsigned int; TId = long int]’
/home/josoga2/triplexator/src/gardener.h:1411:10:   required from ‘void seqan::plant(seqan::Gardener<TId, TSpec>&, const seqan::Pattern<TIndex, seqan::QGramsLookup<TShape, TPatternSpec> >&, TQuerySet&, const TError&, const TSize&, const TDrop&, seqan::MULTIPLE_WORKER) [with TIndex = seqan::Index<seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >, seqan::Tag<seqan::OpenAddressing_> > >; TPatternSpec = const seqan::Tag<seqan::Finder_QGramsLookup_>; TShape = seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >; TQuerySet = seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >; TError = double; TSize = long int; TDrop = unsigned int; TSpec = seqan::Tag<seqan::GardenerUngapped_>; TId = long int; seqan::MULTIPLE_WORKER = seqan::Tag<seqan::_MULTIPLE_WORKER>]’
/home/josoga2/triplexator/src/triplex.h:1998:9:   required from ‘void seqan::_filterTriplex(seqan::Gardener<TId, TGardenerSpec>&, const TPattern&, TQuery&, const seqan::Options&) [with TId = long int; TGardenerSpec = seqan::Tag<seqan::GardenerUngapped_>; TPattern = seqan::Pattern<seqan::Index<seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >, seqan::Tag<seqan::OpenAddressing_> > >, seqan::QGramsLookup<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >, const seqan::Tag<seqan::Finder_QGramsLookup_> > >; TQuery = seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >]’
/home/josoga2/triplexator/src/triplex.h:2088:20:   required from ‘void seqan::_detectTriplexParallelStrands(TMatches&, TPotentials&, const TPattern&, TDuplex&, const TId&, seqan::Options&, seqan::Gardener<TId, TGardenerSpec>) [with TMatches = std::__cxx11::list<seqan::TriplexMatch<long int, long int, double> >; TPotentials = seqan::Map<seqan::Pair<seqan::Pair<unsigned int>, seqan::TriplexPotential<seqan::Pair<unsigned int> > >, seqan::Skiplist<> >; TId = long int; TPattern = seqan::Pattern<seqan::Index<seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >, seqan::Tag<seqan::OpenAddressing_> > >, seqan::QGramsLookup<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >, const seqan::Tag<seqan::Finder_QGramsLookup_> > >; TDuplex = seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >; TGardenerSpec = seqan::Tag<seqan::GardenerUngapped_>]’
/home/josoga2/triplexator/src/triplex.h:3857:34:   required from ‘int seqan::startTriplexSearchSerial(TMotifSet&, const seqan::StringSet<seqan::String<char, seqan::Alloc<void> > >&, const TPattern&, TFile&, TId, seqan::Options&, seqan::Gardener<TId, TGardenerSpec>) [with TMotifSet = seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >; TFile = std::basic_ofstream<char>; TPattern = seqan::Pattern<seqan::Index<seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >, seqan::IndexQGram<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >, seqan::Tag<seqan::OpenAddressing_> > >, seqan::QGramsLookup<seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >, const seqan::Tag<seqan::Finder_QGramsLookup_> > >; TId = long int; TGardenerSpec = seqan::Tag<seqan::GardenerUngapped_>]’
/home/josoga2/triplexator/src/triplexator.cpp:695:41:   required from ‘int seqan::_findTriplex(TMotifSet&, const seqan::StringSet<seqan::String<char, seqan::Alloc<void> > >&, TFile&, seqan::Options&, const TShape&) [with TMotifSet = seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >; TFile = std::basic_ofstream<char>; TShape = seqan::Shape<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::UngappedShape<0> >]’
/home/josoga2/triplexator/src/triplexator.cpp:865:29:   required from ‘int seqan::mapTriplexes(seqan::Options&) [with TOligoSet = seqan::StringSet<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > >; TMotifSet = seqan::StringSet<seqan::ModStringTriplex<seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> >, seqan::String<seqan::SimpleType<unsigned char, seqan::Triplex_>, seqan::Alloc<void> > > >]’
/home/josoga2/triplexator/src/triplexator.cpp:1422:57:   required from here
/home/josoga2/triplexator/src/find_index_qgrams.h:474:9: warning: narrowing conversion of ‘diag’ from ‘__int64 {aka long int}’ to ‘int’ inside { } [-Wnarrowing]
    THit hit = {                //
         ^~~
src/CMakeFiles/triplexator.dir/build.make:62: recipe for target 'src/CMakeFiles/triplexator.dir/triplexator.cpp.o' failed
make[2]: *** [src/CMakeFiles/triplexator.dir/triplexator.cpp.o] Error 1
CMakeFiles/Makefile2:85: recipe for target 'src/CMakeFiles/triplexator.dir/all' failed
make[1]: *** [src/CMakeFiles/triplexator.dir/all] Error 2
Makefile:151: recipe for target 'all' failed
make: *** [all] Error 2

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