SeqAn3  3.0.1
The Modern C++ library for sequence analysis.
output_options.hpp
Go to the documentation of this file.
1 // -----------------------------------------------------------------------------------------------------
2 // Copyright (c) 2006-2020, Knut Reinert & Freie Universit├Ąt Berlin
3 // Copyright (c) 2016-2020, Knut Reinert & MPI f├╝r 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/seqan3/blob/master/LICENSE.md
6 // -----------------------------------------------------------------------------------------------------
7 
13 #pragma once
14 
15 #include <seqan3/core/platform.hpp>
16 
17 namespace seqan3
18 {
19 
22 {
24  bool fasta_legacy_id_marker = false;
26  bool fasta_blank_before_id = true;
28  uint32_t fasta_letters_per_line = 80;
29  //TODO:
30 // bool fasta_charcounts = false;
31 
32 
34  bool fastq_double_id = false;
35 
39  bool add_carriage_return = false;
40 
43 };
44 
45 } // namespace seqan3
seqan3::sequence_file_output_options::fastq_double_id
bool fastq_double_id
Whether to write the ID only '@' or also after '+' line.
Definition: output_options.hpp:34
seqan3::sequence_file_output_options::fasta_blank_before_id
bool fasta_blank_before_id
Insert a single space after ">" (or ";") before the actual ID.
Definition: output_options.hpp:26
seqan3::sequence_file_output_options::embl_genbank_complete_header
bool embl_genbank_complete_header
Complete header given for embl or genbank.
Definition: output_options.hpp:42
seqan3::sequence_file_output_options::fasta_letters_per_line
uint32_t fasta_letters_per_line
Inserts linebreaks after every n-th letter in the sequence; 0 means no linebreaks.
Definition: output_options.hpp:28
seqan3
The main SeqAn3 namespace.
Definition: aligned_sequence_concept.hpp:36
seqan3::sequence_file_output_options
The options type defines various option members that influence the behaviour of all or some formats.
Definition: output_options.hpp:21
seqan3::sequence_file_output_options::add_carriage_return
bool add_carriage_return
The default plain text line-ending is "\n", but on Windows an additional carriage return is recommend...
Definition: output_options.hpp:39
seqan3::sequence_file_output_options::fasta_legacy_id_marker
bool fasta_legacy_id_marker
Begin the ID line with ";" instead of ">" (not recommended).
Definition: output_options.hpp:24
platform.hpp
Provides platform and dependency checks.