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
15namespace 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