fastq_to_fasta
A template for creation of SeqAn3 apps, with a FASTQ to FASTA example app.
adjust_seed.hpp
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1 // --------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2022, Knut Reinert & Freie Universität Berlin
3 // Copyright (c) 2016-2022, Knut Reinert & MPI für molekulare Genetik
4 // This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
5 // shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md
6 // --------------------------------------------------------------------------------------------------
7 
8 #pragma once
9 
10 #include <cstdint>
11 
12 namespace raptor
13 {
14 
15 /*\brief Adjust the default seed such that it does not interfere with the IBF's hashing.
16  *\param kmer_size The used k-mer size. For gapped shapes, this corresponds to the number of set bits (count()).
17  *\param seed The seed.
18  *\details
19  *
20  * The hashing used with the IBF assumes that the input values are uniformly distributed.
21  * However, we use a 64 bit seed, and unless the `kmer_size` is 32, not all 64 bits of the k-mers change.
22  * Hence, we need to shift the seed to the right.
23  *
24  * 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:
25  *
26  * ```
27  * seed = 1111'1011
28  * kmer = 0000'XXXX
29  * ```
30  *
31  * `seed XOR kmer` will then always have 4 leading ones.
32  */
33 static inline constexpr uint64_t adjust_seed(uint8_t const kmer_size,
34  uint64_t const seed = 0x8F3F73B5CF1C9ADEULL) noexcept
35 {
36  return seed >> (64u - 2u * kmer_size);
37 }
38 
39 } // namespace raptor
Definition: adjust_seed.hpp:13