Remove raptor data simulaiton submodule

.gitmodules

@@ -2,15 +2,6 @@
 	path = lib/seqan3
 	url = https://github.com/seqan/seqan3.git
 	branch = master
-[submodule "lib/robin-hood-hashing"]
-	path = lib/robin-hood-hashing
-	url = https://github.com/martinus/robin-hood-hashing.git
-[submodule "lib/raptor"]
-	path = lib/raptor
-	url = https://github.com/seqan/raptor.git
-[submodule "lib/raptor_data_simulation"]
-	path = lib/raptor_data_simulation
-	url = [email protected]:eaasna/raptor_data_simulation.git
 [submodule "lib/seqan"]
 	path = lib/seqan
 	url = [email protected]:seqan/seqan.git

include/raptor/LICENSE.md

@@ -0,0 +1,30 @@
+BSD 3-Clause License
+
+Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
+Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
+All rights reserved.
+
+Redistribution and use in source and binary forms, with or without
+modification, are permitted provided that the following conditions are met:
+
+1. Redistributions of source code must retain the above copyright notice, this
+   list of conditions and the following disclaimer.
+
+2. Redistributions in binary form must reproduce the above copyright notice,
+   this list of conditions and the following disclaimer in the documentation
+   and/or other materials provided with the distribution.
+
+3. Neither the name of the copyright holder nor the names of its
+   contributors may be used to endorse or promote products derived from
+   this software without specific prior written permission.
+
+THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
+DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
+FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
+DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
+SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
+CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
+OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
+OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.

include/raptor/adjust_seed.hpp

@@ -0,0 +1,42 @@
+// --------------------------------------------------------------------------------------------------
+// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
+// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
+// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
+// shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md
+// --------------------------------------------------------------------------------------------------
+
+/*!\file
+ * \brief Provides raptor::adjust_seed.
+ * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
+ */
+
+#pragma once
+
+#include <cstdint>
+
+namespace raptor
+{
+
+/*\brief Adjust the default seed such that it does not interfere with the IBF's hashing.
+ *\param kmer_size The used k-mer size. For gapped shapes, this corresponds to the number of set bits (count()).
+ *\details
+ *
+ * The hashing used with the IBF assumes that the input values are uniformly distributed.
+ * However, we use a 64 bit seed, and unless the `kmer_size` is 32, not all 64 bits of the k-mers change.
+ * Hence, we need to shift the seed to the right.
+ *
+ * For example, using 2-mers and a seed of length 8 bit, the values for the k-mers will only change for the last 4 bits:
+ *
+ * ```
+ * seed = 1111'1011
+ * kmer = 0000'XXXX
+ * ```
+ *
+ * `seed XOR kmer` will then always have 4 leading ones.
+ */
+static inline constexpr uint64_t adjust_seed(uint8_t const kmer_size) noexcept
+{
+    return 0x8F3F73B5CF1C9ADEULL >> (64u - 2u * kmer_size);
+}
+
+} // namespace raptor

include/raptor/dna4_traits.hpp

@@ -0,0 +1,25 @@
+// --------------------------------------------------------------------------------------------------
+// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
+// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
+// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
+// shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md
+// --------------------------------------------------------------------------------------------------
+
+/*!\file
+ * \brief Provides raptor::dna4_traits.
+ * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
+ */
+
+#pragma once
+
+#include <seqan3/io/sequence_file/input.hpp>
+
+namespace raptor
+{
+
+struct dna4_traits : seqan3::sequence_file_input_default_traits_dna
+{
+    using sequence_alphabet = seqan3::dna4;
+};
+
+} // namespace raptor

include/raptor/file_reader.hpp

@@ -0,0 +1,181 @@
+// --------------------------------------------------------------------------------------------------
+// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
+// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
+// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
+// shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md
+// --------------------------------------------------------------------------------------------------
+
+/*!\file
+ * \brief Provides raptor::file_reader.
+ * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
+ */
+
+#pragma once
+
+#include <seqan3/io/sequence_file/input.hpp>
+#include <seqan3/search/views/minimiser_hash.hpp>
+
+#include <raptor/adjust_seed.hpp>
+#include <raptor/dna4_traits.hpp>
+
+namespace raptor
+{
+
+enum class file_types
+{
+    sequence,
+    minimiser
+};
+
+template <file_types file_type>
+class file_reader
+{};
+
+template <>
+class file_reader<file_types::sequence>
+{
+public:
+    file_reader() = default;
+    file_reader(file_reader const &) = default;
+    file_reader(file_reader &&) = default; // GCOVR_EXCL_LINE
+    file_reader & operator=(file_reader const &) = default;
+    file_reader & operator=(file_reader &&) = default;
+    ~file_reader() = default;
+
+    explicit file_reader(seqan3::shape const shape, uint32_t const window_size) :
+        minimiser_view{seqan3::views::minimiser_hash(shape,
+                                                     seqan3::window_size{window_size},
+                                                     seqan3::seed{adjust_seed(shape.count())})}
+    {}
+
+    template <std::output_iterator<uint64_t> it_t>
+    void hash_into(std::vector<std::string> const & filenames, it_t target) const
+    {
+        for (auto && filename : filenames)
+            hash_into(filename, target);
+    }
+
+    template <std::output_iterator<uint64_t> it_t>
+    void hash_into(std::string const & filename, it_t target) const
+    {
+        sequence_file_t fin{filename};
+        for (auto && record : fin)
+            std::ranges::copy(record.sequence() | minimiser_view, target);
+    }
+
+    template <std::output_iterator<uint64_t> it_t>
+    void hash_into_if(std::vector<std::string> const & filenames, it_t target, auto && pred) const
+    {
+        for (auto && filename : filenames)
+            hash_into_if(filename, target, pred);
+    }
+
+    template <std::output_iterator<uint64_t> it_t>
+    void hash_into_if(std::string const & filename, it_t target, auto && pred) const
+    {
+        sequence_file_t fin{filename};
+        for (auto && record : fin)
+            std::ranges::copy_if(record.sequence() | minimiser_view, target, pred);
+    }
+
+    void on_hash(std::vector<std::string> const & filenames, auto && callback) const
+    {
+        for (auto && filename : filenames)
+            on_hash(filename, callback);
+    }
+
+    void on_hash(std::string const & filename, auto && callback) const
+    {
+        sequence_file_t fin{filename};
+        for (auto && record : fin)
+            callback(record.sequence() | minimiser_view);
+    }
+
+    void for_each_hash(std::vector<std::string> const & filenames, auto && callback) const
+    {
+        for (auto && filename : filenames)
+            for_each_hash(filename, callback);
+    }
+
+    void for_each_hash(std::string const & filename, auto && callback) const
+    {
+        sequence_file_t fin{filename};
+        for (auto && record : fin)
+            std::ranges::for_each(record.sequence() | minimiser_view, callback);
+    }
+
+private:
+    using sequence_file_t = seqan3::sequence_file_input<dna4_traits, seqan3::fields<seqan3::field::seq>>;
+    using view_t = decltype(seqan3::views::minimiser_hash(seqan3::shape{}, seqan3::window_size{}, seqan3::seed{}));
+    view_t minimiser_view = seqan3::views::minimiser_hash(seqan3::shape{}, seqan3::window_size{}, seqan3::seed{});
+};
+
+template <>
+class file_reader<file_types::minimiser>
+{
+public:
+    file_reader() = default;
+    file_reader(file_reader const &) = default;
+    file_reader(file_reader &&) = default;
+    file_reader & operator=(file_reader const &) = default;
+    file_reader & operator=(file_reader &&) = default;
+    ~file_reader() = default;
+
+    explicit file_reader(seqan3::shape const, uint32_t const)
+    {}
+
+    template <std::output_iterator<uint64_t> it_t>
+    void hash_into(std::vector<std::string> const & filenames, it_t target) const
+    {
+        for (auto && filename : filenames)
+            hash_into(filename, target);
+    }
+
+    template <std::output_iterator<uint64_t> it_t>
+    void hash_into(std::string const & filename, it_t target) const
+    {
+        std::ifstream fin{filename, std::ios::binary};
+        uint64_t value;
+        while (fin.read(reinterpret_cast<char *>(&value), sizeof(value)))
+        {
+            *target = value;
+            ++target;
+        }
+    }
+
+    template <std::output_iterator<uint64_t> it_t>
+    void hash_into_if(std::vector<std::string> const & filenames, it_t target, auto && pred) const
+    {
+        for (auto && filename : filenames)
+            hash_into_if(filename, target, pred);
+    }
+
+    template <std::output_iterator<uint64_t> it_t>
+    void hash_into_if(std::string const & filename, it_t target, auto && pred) const
+    {
+        std::ifstream fin{filename, std::ios::binary};
+        uint64_t value;
+        while (fin.read(reinterpret_cast<char *>(&value), sizeof(value)))
+            if (pred(value))
+            {
+                *target = value;
+                ++target;
+            }
+    }
+
+    void for_each_hash(std::vector<std::string> const & filenames, auto && callback) const
+    {
+        for (auto && filename : filenames)
+            for_each_hash(filename, callback);
+    }
+
+    void for_each_hash(std::string const & filename, auto && callback) const
+    {
+        std::ifstream fin{filename, std::ios::binary};
+        uint64_t value;
+        while (fin.read(reinterpret_cast<char *>(&value), sizeof(value)))
+            callback(value);
+    }
+};
+
+} // namespace raptor

include/raptor/strong_types.hpp

@@ -0,0 +1,26 @@
+// --------------------------------------------------------------------------------------------------
+// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
+// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
+// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
+// shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md
+// --------------------------------------------------------------------------------------------------
+
+/*!\file
+ * \brief Provides raptor::window.
+ * \author Enrico Seiler <enrico.seiler AT fu-berlin.de>
+ */
+
+#pragma once
+
+#include <cstdint>
+
+namespace raptor
+{
+
+//!\brief Strong type for passing the window size.
+struct window
+{
+    uint32_t v{};
+};
+
+} // namespace raptor