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