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default_configuration.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/configuration/configuration.hpp>
#include <seqan3/search/configuration/detail.hpp>
#include <seqan3/search/configuration/hit.hpp>
#include <seqan3/search/configuration/max_error.hpp>
#include <seqan3/search/configuration/output.hpp>
namespace seqan3::search_cfg
{
constexpr configuration default_configuration = max_error_total{error_count{0}} | max_error_substitution{error_count{0}}
| max_error_insertion{error_count{0}} | max_error_deletion{error_count{0}}
| output_query_id{} | output_reference_id{}
| output_reference_begin_position{} | hit_all{};
} // namespace seqan3::search_cfg
seqan3::configuration
Collection of elements to configure an algorithm.
Definition configuration.hpp:42
seqan3::search_cfg::hit_all
Configuration element to receive all hits within the error bounds.
Definition hit.hpp:31
seqan3::search_cfg::max_error_deletion
Configuration element that represents the number or rate of deletion errors.
Definition max_error.hpp:170
seqan3::search_cfg::max_error_insertion
Configuration element that represents the number or rate of insertion errors.
Definition max_error.hpp:124
seqan3::search_cfg::max_error_total
Configuration element that represents the number or rate of total errors.
Definition max_error.hpp:34
seqan3::search_cfg::output_query_id
Include the query_id in the seqan3::search_result returned by a call to seqan3::search.
Definition search/configuration/output.hpp:28
seqan3::search_cfg::output_reference_begin_position
Include the reference_begin_position in the seqan3::search_result returned by a call to seqan3::searc...
Definition search/configuration/output.hpp:78
seqan3::search_cfg::output_reference_id
Include the reference_id in the seqan3::search_result returned by a call to seqan3::search.
Definition search/configuration/output.hpp:53
configuration.hpp
Provides seqan3::configuration and utility functions.
seqan3::search_cfg::default_configuration
constexpr configuration default_configuration
The default configuration: Compute all exact matches.
Definition default_configuration.hpp:26
hit.hpp
Provides the configuration to define the hit strategies "hit_strata", "hit_all", "hit_all_best",...
max_error.hpp
Provides the configuration for maximum number of errors for all error types.
seqan3::search_cfg
A special sub namespace for the search configurations.
detail.hpp
Provides compatibility matrix for search configurations.
output.hpp
Provides the configuration for the content of the search result.
seqan3::search_cfg::error_count
A strong type of underlying type uint8_t that represents the number of errors.
Definition max_error_common.hpp:29
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