Try replace stellar matcher

include/valik/search/iterate_queries.hpp

@@ -55,37 +55,38 @@ struct adaptor_traits : seqan3::sequence_file_input_default_traits_dna
  * @param arguments Command line arguments.
  * @param queue Shopping cart queue for sending queries over to Stellar search.
  */
-template <typename TSequence>
+template <typename sequence_t>
 void iterate_all_queries(size_t const ref_seg_count,
                          search_arguments const & arguments,
-                         cart_queue<shared_query_record<TSequence>> & queue)
-{
-    seqan3::sequence_file_input<adaptor_traits> fin{std::istringstream{arguments.query_file}, seqan3::format_fasta{}};
-    using record_type = typename decltype(fin)::record_type;
-
-    using sequence_type = std::remove_cvref_t<decltype(std::declval<record_type>().sequence())>;
-    std::vector<sequence_type> rec_vec{};
-    for (auto & record : fin)
+                         cart_queue<shared_query_record<sequence_t>> & queue)
+{    
+    /*
+    std::vector<sequence_type> seq_vec{};
+    for (auto & seq : rec_vec | std::views::transform([](record_type record) { return record.sequence(); }))
     {
-        rec_vec.emplace_back(record.sequence());
+        seq_vec.emplace_back(seq);
     }
 
-    jst::contrib::stellar_matcher<sequence_type> matcher(rec_vec, (double) arguments.error_rate, (unsigned) arguments.minLength);
+    jst::contrib::stellar_matcher<sequence_type> matcher(seq_vec, (double) arguments.error_rate, (unsigned) arguments.minLength);
+    */
 
-    using TId = seqan2::CharString;
-    std::vector<shared_query_record<TSequence>> query_records{};
+    std::vector<shared_query_record<sequence_t>> query_records{};
     constexpr uint64_t chunk_size = (1ULL << 20) * 10;
 
-    seqan2::SeqFileIn inSeqs;
-    if (!open(inSeqs, arguments.query_file.c_str()))
-    {
-        throw std::runtime_error("Failed to open " + arguments.query_file.string() + " file.");
-    }
+    seqan3::sequence_file_input<adaptor_traits> fin{std::istringstream{arguments.query_file}, seqan3::format_fasta{}};
+    using record_type = typename decltype(fin)::record_type;
+    using sequence_type = std::remove_cvref_t<decltype(std::declval<record_type>().sequence())>;
 
     std::set<TId> uniqueIds; // set of short IDs (cut at first whitespace)
     bool idsUnique = true;
 
     size_t seqCount{0};
+    std::vector<record_type> rec_vec{};
+    for (auto & record : fin)
+    {
+        rec_vec.emplace_back(record);
+    }
+
     for (; !atEnd(inSeqs); ++seqCount)
     {
         TSequence seq{};

include/valik/search/query_record.hpp

@@ -30,7 +30,7 @@ template <typename TSequence>
 struct shared_query_record
 {
     std::string sequence_id;
-    std::vector<seqan3::dna4> sequence;
+    std::vector<seqan2::alphabet_adaptor<seqan3::dna4>> sequence;
     seqan2::Segment<TSequence const, seqan2::InfixSegment> querySegment;
     std::shared_ptr<TSequence> underlyingData;
 

include/valik/search/search_local.hpp

@@ -141,8 +141,9 @@ bool search_local(search_arguments & arguments, search_time_statistics & time_st
         }
     }
 
-    using TAlphabet = seqan2::Dna;
-    using TSequence = seqan2::String<TAlphabet>;
+    using TAlphabet = seqan2::alphabet_adaptor<seqan3::dna4>;
+    using TSequence = std::vector<TAlphabet>;
+
     // the queue hands records over from the producer threads (valik prefiltering) to the consumer threads (stellar search) 
     auto queue = cart_queue<shared_query_record<TSequence>>{ref_meta.seg_count, arguments.cart_max_capacity, arguments.max_queued_carts};