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cleanup & version bump to 2.4.0
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@muellan
muellan committed Mar 10, 2024
1 parent a60c498 commit bfbdda5
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Showing 67 changed files with 204 additions and 216 deletions.
2 changes: 1 addition & 1 deletion src/alignment.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Christian Hundt ([email protected])
*
* based on an alignment algorithms implementation by Christian Hundt
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2 changes: 1 addition & 1 deletion src/bitmanip.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/building.cpp
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/building.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/candidate_generation.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/candidate_structs.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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3 changes: 1 addition & 2 deletions src/chunk_allocator.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
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#include <algorithm>
#include <iostream>
#include <memory>
//#include <mutex>
#include <vector>


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2 changes: 1 addition & 1 deletion src/classification.cpp
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/classification.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/classification_statistics.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/cmdline_utility.cpp
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
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2 changes: 1 addition & 1 deletion src/cmdline_utility.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
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2 changes: 1 addition & 1 deletion src/config.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/database.cpp
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/database.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/database_query.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/dna_encoding.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/filesys_utility.cpp
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
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2 changes: 1 addition & 1 deletion src/filesys_utility.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
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2 changes: 1 addition & 1 deletion src/gpu_hashmap.cu
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 Robin Kobus ([email protected])
* Copyright (C) 2016-2022 Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
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3 changes: 1 addition & 2 deletions src/gpu_hashmap.cuh
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 Robin Kobus ([email protected])
* Copyright (C) 2016-2022 Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
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/*************************************************************************//**
* TODO
* @brief (integer) key -> value hashed multimap
* optimized for many values per key (pay attention to max_bucket_size()!
* Each bucket contains only one key and all values mapped to that key.
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2 changes: 1 addition & 1 deletion src/gpu_hashmap_operations.cuh
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 Robin Kobus ([email protected])
* Copyright (C) 2016-2022 Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
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2 changes: 1 addition & 1 deletion src/gpu_result_processing.cuh
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 Robin Kobus ([email protected])
* Copyright (C) 2016-2022 Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
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2 changes: 1 addition & 1 deletion src/hash_dna.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/hash_int.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/hash_multimap.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/host_hashmap.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 Robin Kobus ([email protected])
* Copyright (C) 2016-2022 Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
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2 changes: 1 addition & 1 deletion src/io_error.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
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2 changes: 1 addition & 1 deletion src/io_options.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
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2 changes: 1 addition & 1 deletion src/io_serialize.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/main.cpp
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/matches_per_target.h
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/mode_build.cpp
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/mode_build_query.cpp
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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10 changes: 3 additions & 7 deletions src/mode_help.cpp
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
Expand All @@ -21,19 +21,15 @@


#include "options.h"
#include "filesys_utility.h"

#include <string>
#include <fstream>
#include <iostream>
#include <vector>


namespace mc {


//-------------------------------------------------------------------
void main_mode_help(const cmdline_args& args)
void main_mode_help (const cmdline_args& args)
{
if (args.size() < 3 || args[1] != "help" || args[2] == "help") {

Expand All @@ -42,7 +38,7 @@ void main_mode_help(const cmdline_args& args)
}
else {
std::cout <<
"MetaCache Copyright (C) 2016-2021 André Müller & Robin Kobus\n"
"MetaCache Copyright (C) 2016-2024 André Müller & Robin Kobus\n"
"This program comes with ABSOLUTELY NO WARRANTY.\n"
"This is free software, and you are welcome to redistribute it\n"
"under certain conditions. See the file 'LICENSE' for details.\n\n";
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4 changes: 1 addition & 3 deletions src/mode_info.cpp
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
*
* This program is free software: you can redistribute it and/or modify
* it under the terms of the GNU General Public License as published by
Expand All @@ -29,9 +29,7 @@
#include <array>
#include <iostream>
#include <map>
#include <stdexcept>
#include <string>
#include <typeinfo>
#include <utility>
#include <vector>

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2 changes: 1 addition & 1 deletion src/mode_merge.cpp
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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2 changes: 1 addition & 1 deletion src/mode_query.cpp
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*
* MetaCache - Meta-Genomic Classification Tool
*
* Copyright (C) 2016-2021 André Müller ([email protected])
* Copyright (C) 2016-2024 André Müller ([email protected])
* & Robin Kobus ([email protected])
*
* This program is free software: you can redistribute it and/or modify
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