[misc] track biocpp changes and gcc13

Author: h-2

src/holder_tristate_overload.h

@@ -40,10 +40,8 @@
 #include <bio/ranges/views/slice.hpp>
 #include <bio/ranges/views/translate_single.hpp>
 
-using overload_t = decltype(std::declval<std::vector<bio::alphabet::dna5> &>() | bio::views::translate_single | bio::views::slice(0,1));
-
 template <typename t>
-concept overload_c = std::same_as<std::remove_cvref_t<t>, overload_t>;
+concept overload_c = !std::default_initializable<std::remove_cvref_t<t>>;
 
 namespace seqan
 {

src/mkindex_algo.hpp

@@ -33,6 +33,7 @@
 #include <bio/ranges/views/to_rank.hpp>
 #include <bio/ranges/views/translate.hpp>
 #include <bio/ranges/views/translate_join.hpp>
+#include <bio/ranges/views/validate_char_for.hpp>
 
 #include "mkindex_misc.hpp"
 #include "shared_definitions.hpp"
@@ -116,10 +117,10 @@ auto loadSubjSeqsAndIds(LambdaIndexerOptions const & options)
                                               bio::views::char_to<bio::alphabet::dna5>),
                                      bio::ranges::views::char_conversion_view_t<TOrigAlph>>;
 
-    bio::io::seq::record r{.id = std::string_view{}, .seq = seq_t{}, .qual = std::ignore};
+    using rec_t = decltype(bio::io::seq::record{.id = std::string_view{}, .seq = seq_t{}, .qual = std::ignore});
     bio::io::seq::reader reader{
       options.dbFile,
-      bio::io::seq::reader_options{.record = r, .truncate_ids = options.truncateIDs}
+      bio::io::seq::reader_options{.record = rec_t{}, .truncate_ids = options.truncateIDs}
     };
 
     size_t count = 0;

src/search_datastructures.hpp

@@ -358,15 +358,15 @@ class GlobalDataHolder
     /* output file */
     // SeqAn2 scoring scheme for local alignment of extended seeds. This can be adapted for bisulfite scoring.
     using TScoreSchemeAlign =
-      std::conditional_t<bio::alphabet::nucleotide_alphabet<TTransAlph>,
+      std::conditional_t<bio::alphabet::nucleotide<TTransAlph>,
                          std::conditional_t<c_redAlph == AlphabetEnum::DNA3BS,
                                             seqan::Score<int, seqan::ScoreMatrix<seqan::Dna5, seqan::BisulfiteMatrix>>,
                                             seqan::Score<int, seqan::Simple>>,
                          seqan::Score<int, seqan::ScoreMatrix<seqan::AminoAcid, seqan::ScoreSpecSelectable>>>;
 
     // SeqAn2 scoring scheme for blast statistics (does not work with bisulfite scoring scheme)
     using TScoreSchemeStats =
-      std::conditional_t<bio::alphabet::nucleotide_alphabet<TTransAlph>,
+      std::conditional_t<bio::alphabet::nucleotide<TTransAlph>,
                          seqan::Score<int, seqan::Simple>,
                          seqan::Score<int, seqan::ScoreMatrix<seqan::AminoAcid, seqan::ScoreSpecSelectable>>>;
 

src/seqan2_to_biocpp.hpp

@@ -267,7 +267,7 @@ inline bool operator==(char c, alph_t alph)
     return bio::alphabet::to_char(alph) == c;
 }
 
-template <typename TValue, typename TSequenceValue, typename TSpec, bio::alphabet::aminoacid_alphabet alph_t>
+template <typename TValue, typename TSequenceValue, typename TSpec, bio::alphabet::aminoacid alph_t>
 inline auto score(Score<TValue, ScoreMatrix<TSequenceValue, TSpec>> const & scheme,
                   alph_t const                                              a1,
                   alph_t const                                              a2) noexcept

src/shared_definitions.hpp

@@ -259,7 +259,7 @@ constexpr auto qryTransView = []()
 {
     if constexpr (c_redAlph == AlphabetEnum::DNA3BS)
         return bio::views::type_reduce | bio::views::add_reverse_complement | views::duplicate;
-    else if constexpr (bio::alphabet::nucleotide_alphabet<_alphabetEnumToType<c_redAlph>>)
+    else if constexpr (bio::alphabet::nucleotide<_alphabetEnumToType<c_redAlph>>)
         return bio::views::type_reduce | bio::views::add_reverse_complement;
     else if constexpr (c_origQryAlph == c_transAlph)
         return bio::views::type_reduce;

src/shared_misc.hpp

@@ -82,8 +82,8 @@ constexpr bool all_valid(TRange && r)
 
 inline AlphabetEnum detectSeqFileAlphabet(std::string const & path)
 {
-    bio::io::seq::record r{.id = std::ignore, .seq = std::string_view{}, .qual = std::ignore};
-    bio::io::seq::reader reader{path, bio::io::seq::reader_options{.record = r}};
+    using rec_t = decltype(bio::io::seq::record{.id = std::ignore, .seq = std::string_view{}, .qual = std::ignore});
+    bio::io::seq::reader reader{path, bio::io::seq::reader_options{.record = rec_t{}}};
 
     auto & seq = reader.begin()->seq;