fastq_to_fasta
A template for creation of SeqAn3 apps, with a FASTQ to FASTA example app.
build_arguments.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 #include <vector>
12 
13 #include <seqan3/search/kmer_index/shape.hpp>
14 
15 #include <raptor/strong_types.hpp>
16 
17 namespace raptor
18 {
19 
21 {
22  // Related to k-mers
23  uint8_t kmer_size{20u};
26  std::string shape_string{};
27  seqan3::shape shape{seqan3::ungapped{kmer_size}};
28  bool compute_minimiser{false};
29  bool disable_cutoffs{false};
30 
31  // Related to IBF
32  std::filesystem::path out_path{"./"};
33  std::string size{"1k"};
34  uint64_t bins{64};
35  uint64_t bits{4096};
36  uint64_t hash{2};
37  uint8_t parts{1u};
38  double fpr{0.05};
39  bool compressed{false};
40 
41  // General arguments
42  std::vector<std::vector<std::string>> bin_path{};
43  std::filesystem::path bin_file{};
44  uint8_t threads{1u};
45  bool is_socks{false};
46  bool is_hibf{false};
47  bool is_minimiser{false};
48 };
49 
50 } // namespace raptor
Definition: adjust_seed.hpp:13
Definition: build_arguments.hpp:21
bool is_socks
Definition: build_arguments.hpp:45
uint8_t kmer_size
Definition: build_arguments.hpp:23
bool compute_minimiser
Definition: build_arguments.hpp:28
bool compressed
Definition: build_arguments.hpp:39
std::string size
Definition: build_arguments.hpp:33
uint8_t parts
Definition: build_arguments.hpp:37
std::filesystem::path bin_file
Definition: build_arguments.hpp:43
uint64_t hash
Definition: build_arguments.hpp:36
bool is_minimiser
Definition: build_arguments.hpp:47
uint64_t bits
Definition: build_arguments.hpp:35
window window_size_strong
Definition: build_arguments.hpp:25
seqan3::shape shape
Definition: build_arguments.hpp:27
bool disable_cutoffs
Definition: build_arguments.hpp:29
uint8_t threads
Definition: build_arguments.hpp:44
std::vector< std::vector< std::string > > bin_path
Definition: build_arguments.hpp:42
std::string shape_string
Definition: build_arguments.hpp:26
std::filesystem::path out_path
Definition: build_arguments.hpp:32
double fpr
Definition: build_arguments.hpp:38
uint64_t bins
Definition: build_arguments.hpp:34
bool is_hibf
Definition: build_arguments.hpp:46
uint32_t window_size
Definition: build_arguments.hpp:24
Strong type for passing the window size.
Definition: strong_types.hpp:17