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Read and write VCF with changing some fields. #63

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Irallia opened this issue Oct 18, 2022 · 1 comment
Open

Read and write VCF with changing some fields. #63

Irallia opened this issue Oct 18, 2022 · 1 comment

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@Irallia
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Irallia commented Oct 18, 2022 

#include <bio/var_io/reader.hpp>
#include <bio/var_io/writer.hpp>
...
using namespace std::literals;

/*! \brief Fill ALT fields in VCF with SV types.
 *
 * \param[in] args - command line arguments:\n
 *                   **args.input_file_path** - Mason VCF input file, path to the VCF file\n
 *                   **args.output_file_path** output file - path for the VCF file - *default: standard output*\n
 *
 * \details Takes SVTYPE of SV InDels and fills their ALT fields.
 */
void convert_vcf(cmd_arguments const & args)
{
    bio::var_io::reader reader{args.input_file_path};
    bio::var_io::writer writer{args.output_file_path};

    for (auto & rec : reader) {
            // pos=0 limits the search to the prefix
        if (rec.id().rfind("sim_sv_indel", 0) == 0 && rec.info().front().id == "SVTYPE") {
            if (rec.info().front().value == "INS"sv) {
                rec.alt() = {"<INS>"};
            } else {
                rec.alt() = {"<DEL>"};
            }
            writer.push_back(rec);
        }
    }
}

fails with the following error:

Consolidate compiler generated dependencies of target MasonVcfConverter
[ 94%] Building CXX object src/CMakeFiles/MasonVcfConverter.dir/__/test/benchmark/simulation/mason_vcf_converter.cpp.o
.../test/benchmark/simulation/mason_vcf_converter.cpp: In function 'void convert_vcf(const cmd_arguments&)':
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:46: error: no match for 'operator==' (operand types are 'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} and 'std::basic_string_view<char>')
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                     ~~~~~~~~~~~~~~~~~~~~~~~~ ^~ ~~~~~~~
      |                                        |        |
      |                                        |        std::basic_string_view<char>
      |                                        bio::var_io::info_element_value_type<bio::ownership::shallow> {aka std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>}
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/x86_64-apple-darwin19/bits/c++allocator.h:33,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/allocator.h:46,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ext/new_allocator.h:183:9: note: candidate: 'template<class _Up> constexpr bool __gnu_cxx::operator==(const __gnu_cxx::new_allocator<std::basic_string_view<char> >&, const __gnu_cxx::new_allocator<_Tp>&)' (reversed)
  183 |         operator==(const new_allocator&, const new_allocator<_Up>&)
      |         ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ext/new_allocator.h:183:9: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const __gnu_cxx::new_allocator<_Tp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/x86_64-apple-darwin19/bits/c++allocator.h:33,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/allocator.h:46,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ext/new_allocator.h:183:9: note: candidate: 'template<class _Up> constexpr bool __gnu_cxx::operator==(const __gnu_cxx::new_allocator<float>&, const __gnu_cxx::new_allocator<_Tp>&)' (reversed)
  183 |         operator==(const new_allocator&, const new_allocator<_Up>&)
      |         ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ext/new_allocator.h:183:9: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const __gnu_cxx::new_allocator<_Tp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/x86_64-apple-darwin19/bits/c++allocator.h:33,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/allocator.h:46,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ext/new_allocator.h:183:9: note: candidate: 'template<class _Up> constexpr bool __gnu_cxx::operator==(const __gnu_cxx::new_allocator<int>&, const __gnu_cxx::new_allocator<_Tp>&)' (reversed)
  183 |         operator==(const new_allocator&, const new_allocator<_Up>&)
      |         ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ext/new_allocator.h:183:9: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const __gnu_cxx::new_allocator<_Tp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/x86_64-apple-darwin19/bits/c++allocator.h:33,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/allocator.h:46,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ext/new_allocator.h:183:9: note: candidate: 'template<class _Up> constexpr bool __gnu_cxx::operator==(const __gnu_cxx::new_allocator<short int>&, const __gnu_cxx::new_allocator<_Tp>&)' (reversed)
  183 |         operator==(const new_allocator&, const new_allocator<_Up>&)
      |         ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ext/new_allocator.h:183:9: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const __gnu_cxx::new_allocator<_Tp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_algobase.h:67,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/char_traits.h:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:40,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_iterator.h:1105:5: note: candidate: 'template<class _IteratorL, class _IteratorR, class _Container>  requires requires(_IteratorL __lhs, _IteratorR __rhs) {{__lhs == __rhs} -> decltype(auto) [requires std::convertible_to<<placeholder>, bool>];} constexpr bool __gnu_cxx::operator==(const __gnu_cxx::__normal_iterator<_IteratorL, _Container>&, const __gnu_cxx::__normal_iterator<_IteratorR, _Container>&)' (reversed)
 1105 |     operator==(const __normal_iterator<_IteratorL, _Container>& __lhs,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_iterator.h:1105:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const __gnu_cxx::__normal_iterator<_IteratorL, _Container>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/x86_64-apple-darwin19/bits/c++allocator.h:33,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/allocator.h:46,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ext/new_allocator.h:183:9: note: candidate: 'template<class _Up> constexpr bool __gnu_cxx::operator==(const __gnu_cxx::new_allocator<signed char>&, const __gnu_cxx::new_allocator<_Tp>&)' (reversed)
  183 |         operator==(const new_allocator&, const new_allocator<_Up>&)
      |         ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ext/new_allocator.h:183:9: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const __gnu_cxx::new_allocator<_Tp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/regex:63,
                 from .../lib/b.i.o./include/bio/format/bcf_input_handler.hpp:19,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:20,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/regex.h:1208:5: note: candidate: 'template<class _Bi_iter, class _Ch_traits, class _Ch_alloc> bool std::__cxx11::operator==(const std::__cxx11::sub_match<_BiIter>&, std::__cxx11::__sub_match_string<_Bi_iter, _Ch_traits, _Ch_alloc>&)' (reversed)
 1208 |     operator==(const sub_match<_Bi_iter>& __lhs,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/regex.h:1208:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::__cxx11::sub_match<_BiIter>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/regex:63,
                 from .../lib/b.i.o./include/bio/format/bcf_input_handler.hpp:19,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:20,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/regex.h:1375:5: note: candidate: 'template<class _Bi_iter> bool std::__cxx11::operator==(const std::__cxx11::sub_match<_BiIter>&, const typename std::iterator_traits<_Iter>::value_type*)' (reversed)
 1375 |     operator==(const sub_match<_Bi_iter>& __lhs,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/regex.h:1375:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::__cxx11::sub_match<_BiIter>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/regex:63,
                 from .../lib/b.i.o./include/bio/format/bcf_input_handler.hpp:19,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:20,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/regex.h:1547:5: note: candidate: 'template<class _Bi_iter> bool std::__cxx11::operator==(const std::__cxx11::sub_match<_BiIter>&, const typename std::iterator_traits<_Iter>::value_type&)' (reversed)
 1547 |     operator==(const sub_match<_Bi_iter>& __lhs,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/regex.h:1547:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::__cxx11::sub_match<_BiIter>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_algobase.h:67,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/char_traits.h:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:40,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_iterator.h:494:5: note: candidate: 'template<class _IteratorL, class _IteratorR> constexpr bool std::operator==(const std::reverse_iterator<_IteratorL>&, const std::reverse_iterator<_IteratorR>&) requires requires{{std::operator==::__x->base() == std::operator==::__y->base()} -> decltype(auto) [requires std::convertible_to<<placeholder>, bool>];}' (reversed)
  494 |     operator==(const reverse_iterator<_IteratorL>& __x,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_iterator.h:494:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::reverse_iterator<_IteratorL>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_algobase.h:67,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/char_traits.h:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:40,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_iterator.h:1533:5: note: candidate: 'template<class _IteratorL, class _IteratorR> constexpr bool std::operator==(const std::move_iterator<_IteratorL>&, const std::move_iterator<_IteratorR>&) requires requires{{std::operator==::__x->base() == std::operator==::__y->base()} -> decltype(auto) [requires std::convertible_to<<placeholder>, bool>];}' (reversed)
 1533 |     operator==(const move_iterator<_IteratorL>& __x,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_iterator.h:1533:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::move_iterator<_IteratorL>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/allocator.h:230:5: note: candidate: 'template<class _T1, class _T2> constexpr bool std::operator==(const std::allocator<_CharT>&, const std::allocator<_T2>&)' (reversed)
  230 |     operator==(const allocator<_T1>&, const allocator<_T2>&)
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/allocator.h:230:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::allocator<_CharT>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/basic_string.h:48,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:55,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string_view:540:5: note: candidate: 'constexpr bool std::operator==(std::basic_string_view<_CharT, _Traits>, std::__type_identity_t<std::basic_string_view<_CharT, _Traits> >) [with _CharT = char; _Traits = std::char_traits<char>; std::__type_identity_t<std::basic_string_view<_CharT, _Traits> > = std::basic_string_view<char>]' (reversed)
  540 |     operator==(basic_string_view<_CharT, _Traits> __x,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string_view:541:70: note:   no known conversion for argument 2 from 'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} to 'std::__type_identity_t<std::basic_string_view<char> >' {aka 'std::basic_string_view<char>'}
  541 |                __type_identity_t<basic_string_view<_CharT, _Traits>> __y)
      |                ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:55,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/basic_string.h:6247:5: note: candidate: 'template<class _CharT, class _Traits, class _Alloc> bool std::operator==(const std::__cxx11::basic_string<_CharT, _Traits, _Allocator>&, const _CharT*)' (reversed)
 6247 |     operator==(const basic_string<_CharT, _Traits, _Alloc>& __lhs,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/basic_string.h:6247:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::__cxx11::basic_string<_CharT, _Traits, _Allocator>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/unique_ptr.h:37,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/locale_conv.h:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/locale:43,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_path.h:37,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:45,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/tuple:1513:5: note: candidate: 'template<class ... _TElements, class ... _UElements> constexpr bool std::operator==(const std::tuple<_Tps ...>&, const std::tuple<_UTypes ...>&)' (reversed)
 1513 |     operator==(const tuple<_TElements...>& __t,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/tuple:1513:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::tuple<_Tps ...>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/locale_conv.h:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/locale:43,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_path.h:37,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:45,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/unique_ptr.h:753:5: note: candidate: 'template<class _Tp, class _Dp, class _Up, class _Ep> bool std::operator==(const std::unique_ptr<_Tp, _Dp>&, const std::unique_ptr<_Up, _Ep>&)' (reversed)
  753 |     operator==(const unique_ptr<_Tp, _Dp>& __x,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/unique_ptr.h:753:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::unique_ptr<_Tp, _Dp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/locale_conv.h:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/locale:43,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_path.h:37,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:45,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/unique_ptr.h:760:5: note: candidate: 'template<class _Tp, class _Dp> bool std::operator==(const std::unique_ptr<_Tp, _Dp>&, std::nullptr_t)' (reversed)
  760 |     operator==(const unique_ptr<_Tp, _Dp>& __x, nullptr_t) noexcept
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/unique_ptr.h:760:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::unique_ptr<_Tp, _Dp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/shared_ptr.h:53,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_path.h:46,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:45,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/shared_ptr_base.h:1410:5: note: candidate: 'template<class _Tp1, class _Tp2, __gnu_cxx::_Lock_policy _Lp> bool std::operator==(const std::__shared_ptr<_Tp1, _Lp>&, const std::__shared_ptr<_Tp2, _Lp>&)' (reversed)
 1410 |     operator==(const __shared_ptr<_Tp1, _Lp>& __a,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/shared_ptr_base.h:1410:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::__shared_ptr<_Tp1, _Lp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/shared_ptr.h:53,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_path.h:46,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:45,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/shared_ptr_base.h:1416:5: note: candidate: 'template<class _Tp, __gnu_cxx::_Lock_policy _Lp> bool std::operator==(const std::__shared_ptr<_Tp, _Lp>&, std::nullptr_t)' (reversed)
 1416 |     operator==(const __shared_ptr<_Tp, _Lp>& __a, nullptr_t) noexcept
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/shared_ptr_base.h:1416:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::__shared_ptr<_Tp, _Lp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_path.h:46,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:45,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/shared_ptr.h:437:5: note: candidate: 'template<class _Tp, class _Up> bool std::operator==(const std::shared_ptr<_Tp>&, const std::shared_ptr<_Tp>&)' (reversed)
  437 |     operator==(const shared_ptr<_Tp>& __a, const shared_ptr<_Up>& __b) noexcept
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/shared_ptr.h:437:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::shared_ptr<_Tp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_path.h:46,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:45,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/shared_ptr.h:443:5: note: candidate: 'template<class _Tp> bool std::operator==(const std::shared_ptr<_Tp>&, std::nullptr_t)' (reversed)
  443 |     operator==(const shared_ptr<_Tp>& __a, nullptr_t) noexcept
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/shared_ptr.h:443:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::shared_ptr<_Tp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ranges:44,
                 from .../lib/b.i.o./include/bio/detail/views_eager_split.hpp:18,
                 from .../lib/b.i.o./include/bio/detail/index_tabix.hpp:16,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:18,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/optional:1038:5: note: candidate: 'template<class _Tp, class _Up> constexpr std::__optional_eq_t<_Tp, _Up> std::operator==(const std::optional<_Tp>&, const std::optional<_Up>&)' (reversed)
 1038 |     operator==(const optional<_Tp>& __lhs, const optional<_Up>& __rhs)
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/optional:1038:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::optional<_Tp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ranges:44,
                 from .../lib/b.i.o./include/bio/detail/views_eager_split.hpp:18,
                 from .../lib/b.i.o./include/bio/detail/index_tabix.hpp:16,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:18,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/optional:1098:5: note: candidate: 'template<class _Tp> constexpr bool std::operator==(const std::optional<_Tp>&, std::nullopt_t)' (reversed)
 1098 |     operator==(const optional<_Tp>& __lhs, nullopt_t) noexcept
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/optional:1098:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::optional<_Tp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ranges:44,
                 from .../lib/b.i.o./include/bio/detail/views_eager_split.hpp:18,
                 from .../lib/b.i.o./include/bio/detail/index_tabix.hpp:16,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:18,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/optional:1166:5: note: candidate: 'template<class _Tp, class _Up> constexpr std::__optional_eq_t<_Tp, _Up> std::operator==(const std::optional<_Tp>&, const _Up&)' (reversed)
 1166 |     operator==(const optional<_Tp>& __lhs, const _Up& __rhs)
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/optional:1166:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::optional<_Tp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/ranges:44,
                 from .../lib/b.i.o./include/bio/detail/views_eager_split.hpp:18,
                 from .../lib/b.i.o./include/bio/detail/index_tabix.hpp:16,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:18,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/optional:1172:5: note: candidate: 'template<class _Tp, class _Up> constexpr std::__optional_eq_t<_Up, _Tp> std::operator==(const _Up&, const std::optional<_Tp>&)' (reversed)
 1172 |     operator==(const _Up& __lhs, const optional<_Tp>& __rhs)
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/optional:1172:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const std::optional<_Tp>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/functional:59,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/pstl/glue_algorithm_defs.h:13,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/algorithm:74,
                 from .../lib/b.i.o./include/bio/stream/detail/fast_streambuf_iterator.hpp:18,
                 from .../lib/b.i.o./include/bio/detail/index_tabix.hpp:18,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:18,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/std_function.h:688:5: note: candidate: 'template<class _Res, class ... _Args> bool std::operator==(const std::function<_Res(_ArgTypes ...)>&, std::nullptr_t)' (reversed)
  688 |     operator==(const function<_Res(_Args...)>& __f, nullptr_t) noexcept
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/std_function.h:688:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::function<_Res(_ArgTypes ...)>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:351:3: note: candidate: 'bool std::operator==(const std::error_code&, const std::error_condition&' (reversed)
  351 |   operator==(const error_code& __lhs, const error_condition& __rhs) noexcept
      |   ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:351:32: note:   no known conversion for argument 1 from 'std::basic_string_view<char>' to 'const std::error_code&'
  351 |   operator==(const error_code& __lhs, const error_condition& __rhs) noexcept
      |              ~~~~~~~~~~~~~~~~~~^~~~~
In file included from .../lib/b.i.o./include/bio/detail/reader_base.hpp:20,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:19,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/variant:1223:3: note: candidate: 'template<class ... _Types> constexpr bool std::operator==(const std::variant<_Types ...>&, const std::variant<_Types ...>&)'
 1223 |   _VARIANT_RELATION_FUNCTION_TEMPLATE(==, equal)
      |   ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/variant:1223:3: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::basic_string_view<char>' is not derived from 'const std::variant<_Types ...>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/regex:63,
                 from .../lib/b.i.o./include/bio/format/bcf_input_handler.hpp:19,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:20,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/regex.h:1037:5: note: candidate: 'template<class _BiIter> bool std::__cxx11::operator==(const std::__cxx11::sub_match<_BiIter>&, const std::__cxx11::sub_match<_BiIter>&)'
 1037 |     operator==(const sub_match<_BiIter>& __lhs, const sub_match<_BiIter>& __rhs)
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/regex.h:1037:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const std::__cxx11::sub_match<_BiIter>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/regex:63,
                 from .../lib/b.i.o./include/bio/format/bcf_input_handler.hpp:19,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:20,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/regex.h:2103:5: note: candidate: 'template<class _Bi_iter, class _Alloc> bool std::__cxx11::operator==(const std::__cxx11::match_results<_BiIter, _Alloc>&, const std::__cxx11::match_results<_BiIter, _Alloc>&)'
 2103 |     operator==(const match_results<_Bi_iter, _Alloc>& __m1,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/regex.h:2103:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const std::__cxx11::match_results<_BiIter, _Alloc>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/set:62,
                 from .../lib/seqan3/submodules/sharg-parser/include/sharg/parser.hpp:15,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:5:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_multiset.h:971:5: note: candidate: 'template<class _Key, class _Compare, class _Alloc> bool std::operator==(const std::multiset<_Key, _Compare, _Allocator>&, const std::multiset<_Key, _Compare, _Allocator>&)'
  971 |     operator==(const multiset<_Key, _Compare, _Alloc>& __x,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_multiset.h:971:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const std::multiset<_Key, _Compare, _Allocator>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/set:61,
                 from .../lib/seqan3/submodules/sharg-parser/include/sharg/parser.hpp:15,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:5:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_set.h:985:5: note: candidate: 'template<class _Key, class _Compare, class _Alloc> bool std::operator==(const std::set<_Key, _Compare, _Allocator>&, const std::set<_Key, _Compare, _Allocator>&)'
  985 |     operator==(const set<_Key, _Compare, _Alloc>& __x,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_set.h:985:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const std::set<_Key, _Compare, _Allocator>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/map:62,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/regex:52,
                 from .../lib/b.i.o./include/bio/format/bcf_input_handler.hpp:19,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:20,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_multimap.h:1128:5: note: candidate: 'template<class _Key, class _Tp, class _Compare, class _Alloc> bool std::operator==(const std::multimap<_Key, _Tp, _Compare, _Allocator>&, const std::multimap<_Key, _Tp, _Compare, _Allocator>&)'
 1128 |     operator==(const multimap<_Key, _Tp, _Compare, _Alloc>& __x,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_multimap.h:1128:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const std::multimap<_Key, _Tp, _Compare, _Allocator>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/map:61,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/regex:52,
                 from .../lib/b.i.o./include/bio/format/bcf_input_handler.hpp:19,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:20,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_map.h:1463:5: note: candidate: 'template<class _Key, class _Tp, class _Compare, class _Alloc> bool std::operator==(const std::map<_Key, _Tp, _Compare, _Allocator>&, const std::map<_Key, _Tp, _Compare, _Allocator>&)'
 1463 |     operator==(const map<_Key, _Tp, _Compare, _Alloc>& __x,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_map.h:1463:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const std::map<_Key, _Tp, _Compare, _Allocator>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stack:61,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/regex:47,
                 from .../lib/b.i.o./include/bio/format/bcf_input_handler.hpp:19,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:20,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_stack.h:319:5: note: candidate: 'template<class _Tp, class _Seq> bool std::operator==(const std::stack<_Tp, _Seq>&, const std::stack<_Tp, _Seq>&)'
  319 |     operator==(const stack<_Tp, _Seq>& __x, const stack<_Tp, _Seq>& __y)
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_stack.h:319:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const std::stack<_Tp, _Seq>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/deque:67,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stack:60,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/regex:47,
                 from .../lib/b.i.o./include/bio/format/bcf_input_handler.hpp:19,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:20,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_deque.h:2246:5: note: candidate: 'template<class _Tp, class _Alloc> bool std::operator==(const std::deque<_Tp, _Alloc>&, const std::deque<_Tp, _Alloc>&)'
 2246 |     operator==(const deque<_Tp, _Alloc>& __x, const deque<_Tp, _Alloc>& __y)
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_deque.h:2246:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const std::deque<_Tp, _Alloc>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/iosfwd:40,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:40,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/postypes.h:222:5: note: candidate: 'template<class _StateT> bool std::operator==(const std::fpos<_StateT>&, const std::fpos<_StateT>&)'
  222 |     operator==(const fpos<_StateT>& __lhs, const fpos<_StateT>& __rhs)
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/postypes.h:222:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const std::fpos<_StateT>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_algobase.h:64,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/char_traits.h:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:40,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_pair.h:466:5: note: candidate: 'template<class _T1, class _T2> constexpr bool std::operator==(const std::pair<_T1, _T2>&, const std::pair<_T1, _T2>&)'
  466 |     operator==(const pair<_T1, _T2>& __x, const pair<_T1, _T2>& __y)
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/stl_pair.h:466:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'bio::var_io::info_element_value_type<bio::ownership::shallow>' {aka 'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>'} is not derived from 'const std::pair<_T1, _T2>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/basic_string.h:48,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:55,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string_view:534:5: note: candidate: 'template<class _CharT, class _Traits> constexpr bool std::operator==(std::basic_string_view<_CharT, _Traits>, std::basic_string_view<_CharT, _Traits>)'
  534 |     operator==(basic_string_view<_CharT, _Traits> __x,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string_view:534:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>' is not derived from 'std::basic_string_view<_CharT, _Traits>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/basic_string.h:48,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:55,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string_view:540:5: note: candidate: 'template<class _CharT, class _Traits> constexpr bool std::operator==(std::basic_string_view<_CharT, _Traits>, std::__type_identity_t<std::basic_string_view<_CharT, _Traits> >)'
  540 |     operator==(basic_string_view<_CharT, _Traits> __x,
      |     ^~~~~~~~
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string_view:540:5: note:   template argument deduction/substitution failed:
.../test/benchmark/simulation/mason_vcf_converter.cpp:61:49: note:   'std::variant<char, signed char, short int, int, float, std::basic_string_view<char, std::char_traits<char> >, std::vector<signed char, std::allocator<signed char> >, std::vector<short int, std::allocator<short int> >, std::vector<int, std::allocator<int> >, std::vector<float, std::allocator<float> >, std::vector<std::basic_string_view<char, std::char_traits<char> >, std::allocator<std::basic_string_view<char, std::char_traits<char> > > >, bool>' is not derived from 'std::basic_string_view<_CharT, _Traits>'
   61 |                 if (rec.info().front().value == "INS"sv) {
      |                                                 ^~~~~~~
In file included from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/string:55,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/stdexcept:39,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/system_error:41,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/fs_fwd.h:35,
                 from /usr/local/Cellar/gcc/11.2.0_3/include/c++/11/filesystem:44,
                 from .../lib/b.i.o./include/bio/var_io/reader.hpp:16,
                 from .../test/benchmark/simulation/mason_vcf_converter.cpp:1:
/usr/local/Cellar/gcc/11.2.0_3/include/c++/11/bits/basic_string.h:6225:5: note: candidate: 'template<class _CharT, class _Traits, class _Alloc> bool std::operator==(const std::__cxx11::basic_string<_CharT, _Traits, _Allocator>&, const std::__cxx11::basic_string<_CharT, _Traits, _Allocator>&)'
 6225 |     operator==(const basic_string<_CharT, _Traits, _Alloc>& __lhs,
      |     ^~~~~~~~
...
make[2]: *** [src/CMakeFiles/MasonVcfConverter.dir/__/test/benchmark/simulation/mason_vcf_converter.cpp.o] Error 1
make[1]: *** [src/CMakeFiles/MasonVcfConverter.dir/all] Error 2
make: *** [all] Error 2

My current solution is now:

void convert_vcf(cmd_arguments const & args)
{
    bio::var_io::reader reader{args.input_file_path};
    bio::var_io::writer writer{args.output_file_path};

    for (auto & rec : reader) {

        if (rec.id().starts_with("sim_sv_indel")) {
            for (auto & info : rec.info()) {
                if (info.id != "SVTYPE") continue;
                if(auto* s = std::get_if<std::string_view>(&info.value)) {
                    std::string alt = "<" + std::string{*s} + ">";
                    rec.alt() = {alt};
                }
            }
            writer.push_back(rec);
        } else {
            if (rec.id().rfind("sim_sv_indel", 0) == 0 ) {
                seqan3::debug_stream << rec.info().front().id << "\n";
            }
        }
    }
}
@h-2
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h-2 commented Oct 18, 2022

I have double-checked this and variant<..., string_view, ...> is indeed not comparable with string_view. So if you want comparison, you would need to compare with bio::io::var_io::info_element_value_type{"INS"} which is arguably not very nice.
The workaround you chose is also very valid, and probably what I would recommend, too!

However, I see another problem with the code:

            for (auto & info : rec.info()) {
                if (info.id != "SVTYPE") continue;
                if(auto* s = std::get_if<std::string_view>(&info.value)) {
                    std::string alt = "<" + std::string{*s} + ">";
                    rec.alt() = {alt};
                }
            }
            writer.push_back(rec);

I think you are using the default records, which means that alt is std::vector<std::string_view>. You are assigning a std::string to this within the inner if-statement. That string goes out-of-scope at the end of the if-statement, so the string_view is "dangling" when you push the record to the writer.

You can fix this by defining alt in the same scope that you call push_back()... but if you do bigger changes to the record, it is always recommended to create a deep record instead.

The current main-branch has easy-to-use preset for this.

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@h-2 @Irallia