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
16
17namespace 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