fastq_to_fasta
A template for creation of SeqAn3 apps, with a FASTQ to FASTA example app.
upgrade_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 namespace raptor
16 {
17 
19 {
20  uint32_t window_size{};
21  uint8_t kmer_size{};
22  seqan3::shape shape{};
23  uint8_t parts{1u};
24  bool compressed{false};
25 
26  std::filesystem::path bin_file{};
27  std::filesystem::path in_file{};
28  std::filesystem::path out_file{};
29 
30  std::vector<std::vector<std::string>> bin_path{};
31 };
32 
33 } // namespace raptor
Definition: adjust_seed.hpp:13
Definition: upgrade_arguments.hpp:19
uint8_t parts
Definition: upgrade_arguments.hpp:23
uint32_t window_size
Definition: upgrade_arguments.hpp:20
uint8_t kmer_size
Definition: upgrade_arguments.hpp:21
std::filesystem::path in_file
Definition: upgrade_arguments.hpp:27
std::vector< std::vector< std::string > > bin_path
Definition: upgrade_arguments.hpp:30
seqan3::shape shape
Definition: upgrade_arguments.hpp:22
std::filesystem::path out_file
Definition: upgrade_arguments.hpp:28
std::filesystem::path bin_file
Definition: upgrade_arguments.hpp:26
bool compressed
Definition: upgrade_arguments.hpp:24