fastq_to_fasta
A template for creation of SeqAn3 apps, with a FASTQ to FASTA example app.
threshold_parameters.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 <filesystem>
11 
12 #include <seqan3/search/kmer_index/shape.hpp>
13 
14 namespace raptor::threshold
15 {
16 
18 {
19  // Basic.
20  uint32_t window_size{};
21  seqan3::shape shape{};
22  uint64_t pattern_size{};
23 
24  // Threshold.
25  uint8_t errors{}; // threshold_kinds::(probabilistic|lemma)
26  double percentage{std::numeric_limits<double>::quiet_NaN()}; // threshold_kinds::percentage
27  double p_max{}; // threshold_kinds::probabilistic
28  double fpr{}; // threshold_kinds::probabilistic
29  double tau{}; // threshold_kinds::probabilistic
30 
31  // Cache results.
33  std::filesystem::path output_directory{};
34 };
35 
36 } // namespace raptor::threshold
Definition: forward_strand_minimiser.hpp:19
Definition: search_arguments.hpp:22
Definition: threshold_parameters.hpp:18
double tau
Definition: threshold_parameters.hpp:29
std::filesystem::path output_directory
Definition: threshold_parameters.hpp:33
uint32_t window_size
Definition: threshold_parameters.hpp:20
double percentage
Definition: threshold_parameters.hpp:26
double fpr
Definition: threshold_parameters.hpp:28
uint8_t errors
Definition: threshold_parameters.hpp:25
double p_max
Definition: threshold_parameters.hpp:27
bool cache_thresholds
Definition: threshold_parameters.hpp:32
seqan3::shape shape
Definition: threshold_parameters.hpp:21