Merge pull request #14 from seqan/coverage

Coverage

include/compare.h

@@ -18,7 +18,7 @@ inline constexpr static uint64_t adjust_seed(uint8_t const kmer_size, uint64_t c
     return seed >> (64u - 2u * kmer_size);
 }
 
-enum methods {kmer = 0, minimiser, strobemer};
+enum methods {kmer = 0, minimiser, modmers, strobemer};
 
 struct minimiser_arguments
 {

include/minimiser_hash_distance.hpp

@@ -0,0 +1,114 @@
+// -----------------------------------------------------------------------------------------------------
+// Copyright (c) 2006-2021, Knut Reinert & Freie Universität Berlin
+// Copyright (c) 2016-2021, 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/seqan3/blob/master/LICENSE.md
+// -----------------------------------------------------------------------------------------------------
+
+/*!\file
+ * \author Mitra Darvish <mitra.darvish AT fu-berlin.de>
+ * \brief Provides seqan3::views::minimiser_distance_hash.
+ */
+
+#pragma once
+
+#include <seqan3/alphabet/views/complement.hpp>
+#include <seqan3/core/detail/strong_type.hpp>
+#include <seqan3/search/views/kmer_hash.hpp>
+#include <seqan3/search/views/minimiser_hash.hpp>
+
+#include "minimiser_distance.hpp"
+
+
+namespace seqan3::detail
+{
+//!\brief seqan3::views::minimiser_distance_hash's range adaptor object type (non-closure).
+//!\ingroup search_views
+struct minimiser_distance_hash_fn
+{
+    /*!\brief Store the shape and the window size and return a range adaptor closure object.
+    * \param[in] shape       The seqan3::shape to use for hashing.
+    * \param[in] window_size The windows size to use.
+    * \throws std::invalid_argument if the size of the shape is greater than the `window_size`.
+    * \returns               A range of converted elements.
+    */
+    constexpr auto operator()(shape const & shape, window_size const window_size) const
+    {
+        return seqan3::detail::adaptor_from_functor{*this, shape, window_size};
+    }
+
+    /*!\brief Store the shape, the window size and the seed and return a range adaptor closure object.
+    * \param[in] shape       The seqan3::shape to use for hashing.
+    * \param[in] window_size The size of the window.
+    * \param[in] seed        The seed to use.
+    * \throws std::invalid_argument if the size of the shape is greater than the `window_size`.
+    * \returns               A range of converted elements.
+    */
+    constexpr auto operator()(shape const & shape, window_size const window_size, seed const seed) const
+    {
+        return seqan3::detail::adaptor_from_functor{*this, shape, window_size, seed};
+    }
+
+    /*!\brief Call the view's constructor with the underlying view, a seqan3::shape and a window size as argument.
+     * \param[in] urange      The input range to process. Must model std::ranges::viewable_range and the reference type
+     *                        of the range must model seqan3::semialphabet.
+     * \param[in] shape       The seqan3::shape to use for hashing.
+     * \param[in] window_size The size of the window.
+     * \param[in] seed        The seed to use.
+     * \throws std::invalid_argument if the size of the shape is greater than the `window_size`.
+     * \returns               A range of converted elements.
+     */
+    template <std::ranges::range urng_t>
+    constexpr auto operator()(urng_t && urange,
+                              shape const & shape,
+                              window_size const window_size,
+                              seed const seed = seqan3::seed{0x8F3F73B5CF1C9ADE}) const
+    {
+        static_assert(std::ranges::viewable_range<urng_t>,
+            "The range parameter to views::minimiser_distance_hash cannot be a temporary of a non-view range.");
+        static_assert(std::ranges::forward_range<urng_t>,
+            "The range parameter to views::minimiser_distance_hash must model std::ranges::forward_range.");
+        static_assert(semialphabet<std::ranges::range_reference_t<urng_t>>,
+            "The range parameter to views::minimiser_distance_hash must be over elements of seqan3::semialphabet.");
+
+        if (shape.size() > window_size.get())
+            throw std::invalid_argument{"The size of the shape cannot be greater than the window size."};
+
+        auto forward_strand = std::forward<urng_t>(urange) | seqan3::views::kmer_hash(shape)
+                                                           | std::views::transform([seed] (uint64_t i)
+                                                                                  {return i ^ seed.get();});
+
+        auto reverse_strand = std::forward<urng_t>(urange) | seqan3::views::complement
+                                                           | std::views::reverse
+                                                           | seqan3::views::kmer_hash(shape)
+                                                           | std::views::transform([seed] (uint64_t i)
+                                                                                  {return i ^ seed.get();})
+                                                           | std::views::reverse;
+
+        return minimiser_distance_view(forward_strand, reverse_strand, window_size.get() - shape.size() + 1);
+    }
+};
+
+} // namespace seqan3::detail
+
+
+/*!\name Alphabet related views
+ * \{
+ */
+
+/*!\brief                    Computes the distance of minimisers for a range with a given shape, window size and seed.
+ * \tparam urng_t            The type of the range being processed.
+ * \param[in] urange         The range being processed. [parameter is omitted in pipe notation]
+ * \param[in] shape          The seqan3::shape that determines how to compute the hash value.
+ * \param[in] window_size    The window size to use.
+ * \param[in] seed           The seed used to skew the hash values. Default: 0x8F3F73B5CF1C9ADE.
+ * \returns                  A range of `size_t` where each value is the minimiser of the resp. window.
+ *                           See below for the properties of the returned range.
+ * \ingroup utility_views
+ *
+ * \details
+ * For more information look into seqan3::views::minimiser_hash
+ */
+inline constexpr auto minimiser_hash_distance = seqan3::detail::minimiser_distance_hash_fn{};
+
+//!\}