// SPDX-FileCopyrightText: 2006-2024 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2024 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: CC0-1.0

#include <seqan3/alphabet/nucleotide/dna4.hpp>
#include <seqan3/core/debug_stream.hpp>
#include <seqan3/search/views/minimiser_hash.hpp>

using namespace seqan3::literals;

int main()
{
    std::vector<seqan3::dna4> text{"CCACGTCGACGGTT"_dna4};

    // Here a consecutive shape with size 4 (so the k-mer size is 4) and a window size of 8 is used. The seed is set
    // to 0, so lexicographical ordering is used for demonstration purposes.
    auto minimisers =
        text
        | seqan3::views::minimiser_hash(seqan3::shape{seqan3::ungapped{4}}, seqan3::window_size{8}, seqan3::seed{0});
    seqan3::debug_stream << minimisers << '\n';
    // This leads to [27,97,26,22,5] representing the k-mers [ACGT, CGAC, ACGG, accg, aacc], smaller case k-mers are
    // coming from the reverse strand.

    // Here a gapped shape with size 5 (and a k-mer size of 3) and a window size of 8 is used. The seed is set
    // to 0, so lexicographical ordering is used for demonstration purposes.
    auto minimisers2 = text | seqan3::views::minimiser_hash(0b10101_shape, seqan3::window_size{8}, seqan3::seed{0});
    seqan3::debug_stream << minimisers2 << '\n';
    // This leads to [9, 18, 7, 6] representing the k-mers [A.G.C, C.A.G, a.c.t, a.c.g]
}
