Fix/issue_3264

include/seqan3/alphabet/aminoacid/aminoacid_base.hpp

@@ -11,6 +11,7 @@
 
 #include <seqan3/alphabet/alphabet_base.hpp>
 #include <seqan3/alphabet/aminoacid/concept.hpp>
+#include <seqan3/alphabet/detail/concept.hpp>
 #include <seqan3/alphabet/detail/convert.hpp>
 #include <seqan3/utility/char_operations/transform.hpp>
 
@@ -69,6 +70,7 @@ class aminoacid_base : public aminoacid_empty_base, public alphabet_base<derived
     template <typename other_aa_type>
         requires (!std::same_as<aminoacid_base, other_aa_type>)
               && (!std::same_as<derived_type, other_aa_type>) && aminoacid_alphabet<other_aa_type>
+              && detail::convertable_to_through_char_representation<other_aa_type, derived_type>
     explicit constexpr aminoacid_base(other_aa_type const other) noexcept
     {
         if constexpr (is_constexpr_default_constructible_v<other_aa_type>

include/seqan3/alphabet/detail/concept.hpp

@@ -11,6 +11,7 @@
 
 #include <concepts>
 
+#include <seqan3/alphabet/concept.hpp>
 #include <seqan3/core/platform.hpp>
 
 namespace seqan3::detail
@@ -54,4 +55,18 @@ concept weakly_ordered_with =
     };
 //!\endcond
 
+/*!\interface seqan3::detail::convertable_to_through_char_representation <>
+ * \ingroup alphabet
+ * \tparam from_t The type to convert from.
+ * \tparam to_t   The type to convert to.
+ * \brief Checks whether `from_t` can be converted through `to_t` using their char representation.
+ *
+ * Requires that both `from_t` and `to_t` are alphabets and additionally, that `from_t` is default constructible.
+ */
+//!\cond
+template <typename from_t, typename to_t>
+concept convertable_to_through_char_representation =
+    alphabet<from_t> && alphabet<to_t> && std::default_initializable<from_t>;
+//!\endcond
+
 } // namespace seqan3::detail

include/seqan3/alphabet/detail/convert.hpp

@@ -13,7 +13,7 @@
 
 #include <array>
 
-#include <seqan3/alphabet/concept.hpp>
+#include <seqan3/alphabet/detail/concept.hpp>
 
 // ============================================================================
 // conversion to/from char/rank types
@@ -25,11 +25,12 @@ namespace seqan3::detail
 // clang-format off
 /*!\brief A precomputed conversion table for two alphabets based on their char representations.
  * \ingroup alphabet
- * \tparam in_t The type of the input, must satisfy seqan3::alphabet.
+ * \tparam in_t The type of the input, must satisfy seqan3::alphabet and must be default initializable.
  * \tparam out_t The type of the output, must satisfy seqan3::alphabet.
  * \hideinitializer
  */
-template <alphabet in_t, alphabet out_t>
+template <typename in_t, typename out_t>
+    requires convertable_to_through_char_representation<in_t, out_t>
 constexpr std::array<out_t, alphabet_size<in_t>> convert_through_char_representation
 {
     []() constexpr {

include/seqan3/alphabet/nucleotide/nucleotide_base.hpp

@@ -10,6 +10,7 @@
 #pragma once
 
 #include <seqan3/alphabet/alphabet_base.hpp>
+#include <seqan3/alphabet/detail/concept.hpp>
 #include <seqan3/alphabet/detail/convert.hpp>
 #include <seqan3/alphabet/nucleotide/concept.hpp>
 #include <seqan3/utility/char_operations/transform.hpp>
@@ -77,6 +78,7 @@ class nucleotide_base : public alphabet_base<derived_type, size, char>
     template <typename other_nucl_type>
         requires (!std::same_as<nucleotide_base, other_nucl_type>)
               && (!std::same_as<derived_type, other_nucl_type>) && nucleotide_alphabet<other_nucl_type>
+              && detail::convertable_to_through_char_representation<other_nucl_type, derived_type>
     explicit constexpr nucleotide_base(other_nucl_type const & other) noexcept
     {
         static_cast<derived_type &>(*this) =

test/unit/alphabet/container/bitpacked_sequence_test.cpp

@@ -4,6 +4,8 @@
 
 #include <gtest/gtest.h>
 
+#include <vector>
+
 #include <seqan3/alphabet/composite/alphabet_variant.hpp>
 #include <seqan3/alphabet/container/bitpacked_sequence.hpp>
 #include <seqan3/alphabet/nucleotide/concept.hpp>
@@ -51,3 +53,14 @@ TEST(bitpacked_sequence_test, issue371)
     auto end = source.end();
     [[maybe_unused]] bool result = it != end; // This line causes error.
 }
+
+// https://github.com/seqan/seqan3/issues/3264
+TEST(bitpacked_sequence_test, issue3264)
+{
+    using namespace seqan3::literals;
+
+    seqan3::bitpacked_sequence<seqan3::dna4> source{"ACGGTCAGGTTC"_dna4};
+    auto it = source.begin();
+    seqan3::dna4 val = static_cast<seqan3::dna4>(*it); // this line caused the compiler error
+    EXPECT_EQ(val, 'A'_dna4);
+}

test/unit/search/fm_index_cursor/CMakeLists.txt

@@ -6,3 +6,4 @@ seqan3_test (fm_index_cursor_test.cpp)
 seqan3_test (fm_index_cursor_collection_test.cpp)
 seqan3_test (bi_fm_index_cursor_test.cpp)
 seqan3_test (bi_fm_index_cursor_collection_test.cpp)
+seqan3_test (extend_bitpacked_query_sequence_test.cpp)

test/unit/search/fm_index_cursor/extend_bitpacked_query_sequence_test.cpp

@@ -0,0 +1,29 @@
+// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
+// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
+// SPDX-License-Identifier: BSD-3-Clause
+
+#include <gtest/gtest.h>
+
+#include <vector>
+
+#include <seqan3/alphabet/container/bitpacked_sequence.hpp>
+#include <seqan3/alphabet/nucleotide/dna4.hpp>
+#include <seqan3/search/fm_index/fm_index.hpp>
+#include <seqan3/utility/views/slice.hpp>
+
+#include "../helper.hpp"
+
+TEST(fm_index_cursor_test, extend_right_with_bitpacked_sequence)
+{
+    using namespace seqan3::literals;
+    using result_t = std::vector<std::pair<uint64_t, uint64_t>>;
+
+    seqan3::bitpacked_sequence<seqan3::dna4> seq{"ACGGTCAGGTTC"_dna4};
+    seqan3::fm_index index{seq};
+
+    auto bitpacked_query = seqan3::views::slice(seq, 1, 4);
+
+    auto it = index.cursor();
+    it.extend_right(bitpacked_query); // this line caused the compile time error
+    EXPECT_EQ(seqan3::uniquify(it.locate()), (result_t{{0, 1}}));
+}