adjust_seed.hpp

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// --------------------------------------------------------------------------------------------------
// 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/chopper/blob/main/LICENSE.md
// --------------------------------------------------------------------------------------------------
 
#pragma once
 
#include <cstdint>
 
namespace chopper
{
 
/*\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 chopper