Raptor
3.0.0-rc.1
A fast and space-efficient pre-filter for querying very large collections of nucleotide sequences
upgrade_arguments.hpp
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// --------------------------------------------------------------------------------------------------
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// Copyright (c) 2006-2023, Knut Reinert & Freie Universität Berlin
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// Copyright (c) 2016-2023, Knut Reinert & MPI für molekulare Genetik
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// This file may be used, modified and/or redistributed under the terms of the 3-clause BSD-License
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// shipped with this file and also available at: https://github.com/seqan/raptor/blob/main/LICENSE.md
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// --------------------------------------------------------------------------------------------------
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#pragma once
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#include <
filesystem
>
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#include <
vector
>
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#include <seqan3/search/kmer_index/shape.hpp>
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namespace
raptor
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{
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struct
upgrade_arguments
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{
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uint32_t window_size{};
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seqan3::shape shape{};
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bool
compressed{};
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bool
input_is_minimiser{};
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uint8_t parts{1u};
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uint8_t threads{1u};
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double
fpr{
std::numeric_limits<double>::quiet_NaN
()};
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std::filesystem::path
bin_file{};
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std::filesystem::path
index_file{};
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std::filesystem::path
output_file{};
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std::vector<std::vector<std::string>
> bin_path{};
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};
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}
// namespace raptor
filesystem
std::filesystem::path
std::numeric_limits::quiet_NaN
T quiet_NaN(T... args)
raptor::upgrade_arguments
Definition:
upgrade_arguments.hpp:24
vector
raptor
argument_parsing
upgrade_arguments.hpp
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