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sequence_file/output_options.hpp
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// SPDX-FileCopyrightText: 2006-2025 Knut Reinert & Freie Universität Berlin
// SPDX-FileCopyrightText: 2016-2025 Knut Reinert & MPI für molekulare Genetik
// SPDX-License-Identifier: BSD-3-Clause
#pragma once
#include <seqan3/core/platform.hpp>
namespace seqan3
{
struct sequence_file_output_options
{
bool fasta_legacy_id_marker = false;
bool fasta_blank_before_id = false;
uint32_t fasta_letters_per_line = 80;
//TODO:
// bool fasta_charcounts = false;
bool fastq_double_id = false;
bool add_carriage_return = false;
bool embl_genbank_complete_header = false;
};
} // namespace seqan3
seqan3
The main SeqAn3 namespace.
Definition aligned_sequence_concept.hpp:26
platform.hpp
Provides platform and dependency checks.
seqan3::sequence_file_output_options
The options type defines various option members that influence the behaviour of all or some formats.
Definition sequence_file/output_options.hpp:23
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 sequence_file/output_options.hpp:29
seqan3::sequence_file_output_options::fasta_legacy_id_marker
bool fasta_legacy_id_marker
Begin the ID line with ";" instead of ">" (not recommended).
Definition sequence_file/output_options.hpp:25
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 sequence_file/output_options.hpp:39
seqan3::sequence_file_output_options::embl_genbank_complete_header
bool embl_genbank_complete_header
Complete header given for embl or genbank.
Definition sequence_file/output_options.hpp:42
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 sequence_file/output_options.hpp:27
seqan3::sequence_file_output_options::fastq_double_id
bool fastq_double_id
Whether to write the ID only '@' or also after '+' line.
Definition sequence_file/output_options.hpp:34
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