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Prerel301 #232

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merged 4 commits into from
Aug 5, 2024
Merged

Prerel301 #232

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e678917
[misc] bump version
h-2 Aug 4, 2024
6ac098f
[misc] update citation and copyright
h-2 Aug 4, 2024
6b9ffa0
[doc] fix documentation for --input-alphabet
h-2 Aug 4, 2024
3f3bbfb
[ci] update macos runner to -13
h-2 Aug 5, 2024
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2 changes: 1 addition & 1 deletion src/CMakeLists.txt
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Expand Up @@ -12,7 +12,7 @@

# change this after every release
set (SEQAN_APP_VERSION_MAJOR "3")
set (SEQAN_APP_VERSION_MINOR "0")
set (SEQAN_APP_VERSION_MINOR "1")
set (SEQAN_APP_VERSION_PATCH "0")

# don't change the following
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2 changes: 1 addition & 1 deletion src/bisulfite_scoring.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2019, Sara Hetzel <hetzel @ molgen.mpg.de>
// Copyright (c) 2019-2024, Sara Hetzel <hetzel @ molgen.mpg.de>
// Copyright (c) 2016-2019, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/evaluate_bisulfite_alignment.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2019, Sara Hetzel and MPI für Molekulare Genetik
// Copyright (c) 2019-2024, Sara Hetzel and MPI für Molekulare Genetik
// All rights reserved.
//
// This file is part of Lambda.
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2 changes: 1 addition & 1 deletion src/lambda.cpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/mkindex.cpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/mkindex.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/mkindex_algo.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/mkindex_misc.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/mkindex_options.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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4 changes: 2 additions & 2 deletions src/search.cpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
Expand Down Expand Up @@ -208,7 +208,7 @@ void argConv0(LambdaOptions & options)

// query file
if (options.qryOrigAlphabet ==
AlphabetEnum::DNA4) // means "auto", as dna4 not valid as argument to --query-alphabet
AlphabetEnum::DNA4) // means "auto", as dna4 not valid as argument to --input-alphabet
{
myPrint(options, 1, "Detecting query alphabet... ");
options.qryOrigAlphabet = detectSeqFileAlphabet(options.queryFile);
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2 changes: 1 addition & 1 deletion src/search.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/search_algo.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2019, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2019, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/search_datastructures.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/search_misc.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/search_options.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/search_output.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/shared_definitions.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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6 changes: 3 additions & 3 deletions src/shared_misc.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
Expand Down Expand Up @@ -94,8 +94,8 @@ inline AlphabetEnum detectSeqFileAlphabet(std::string const & path)
else if (all_valid<bio::alphabet::dna15>(seq))
{
std::cerr << "\nWARNING: You query file was detected as non-standard DNA, but it could be AminoAcid, too.\n"
"To explicitly read as AminoAcid, add '--query-alphabet aminoacid'.\n"
"To ignore and disable this warning, add '--query-alphabet dna5'.\n";
"To explicitly read as AminoAcid, add '--input-alphabet aminoacid'.\n"
"To ignore and disable this warning, add '--input-alphabet dna5'.\n";
return AlphabetEnum::DNA5;
}
else if (all_valid<bio::alphabet::aa27>(seq))
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8 changes: 4 additions & 4 deletions src/shared_options.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
Expand Down Expand Up @@ -96,12 +96,12 @@ inline void sharedSetup(sharg::parser & parser)
// Set short description, version, and date
parser.info.version = SEQAN_APP_VERSION;
parser.info.date = __DATE__;
parser.info.citation = "Hauswedell et al (2014); doi: 10.1093/bioinformatics/btu439";
parser.info.citation = "Hauswedell & Hetzal et al (2024); doi: 10.1093/bioinformatics/btae097";
parser.info.short_copyright =
"2013-2020 Hannes Hauswedell, released under the GNU AGPL v3 (or later); "
"2013-2024 Hannes Hauswedell & Sara Hetzel, released under the GNU AGPL v3 (or later); "
"2016-2020 Knut Reinert and Freie Universität Berlin, released under the 3-clause-BSDL";
parser.info.long_copyright =
" Copyright (c) 2013-2020, Hannes Hauswedell\n"
" Copyright (c) 2013-2024, Hannes Hauswedell & Sara Hetzel\n"
" All rights reserved.\n"
"\n"
" This program is free software: you can redistribute it and/or modify\n"
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2 changes: 1 addition & 1 deletion src/view_dna_n_to_random.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2019, Sara Hetzel and MPI für Molekulare Genetik
// Copyright (c) 2019-2024, Sara Hetzel and MPI für Molekulare Genetik
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/view_duplicate.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2019, Sara Hetzel and MPI für Molekulare Genetik
// Copyright (c) 2019-2024, Sara Hetzel and MPI für Molekulare Genetik
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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2 changes: 1 addition & 1 deletion src/view_reduce_to_bisulfite.hpp
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// ==========================================================================
// lambda
// ==========================================================================
// Copyright (c) 2019, Sara Hetzel and MPI für Molekulare Genetik
// Copyright (c) 2019-2024, Sara Hetzel and MPI für Molekulare Genetik
// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
// All rights reserved.
//
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