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Merge pull request #232 from h-2/prerel301
Prerel301
2 parents 0055ca9 + 3f3bbfb commit 7512a3f

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+32
-32
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‎.github/workflows/ci_macos.yml

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@@ -16,15 +16,15 @@ defaults:
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jobs:
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build:
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name: ${{ matrix.name }}
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runs-on: macos-11
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runs-on: macos-13
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timeout-minutes: 120
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strategy:
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fail-fast: false
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matrix:
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include:
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- name: "gcc13"
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cxx: "g++-13"
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cc: "gcc-13"
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- name: "gcc12"
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cxx: "g++-12"
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cc: "gcc-12"
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build_type: Release
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- name: "gcc11"

‎src/CMakeLists.txt

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# change this after every release
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set (SEQAN_APP_VERSION_MAJOR "3")
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set (SEQAN_APP_VERSION_MINOR "0")
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set (SEQAN_APP_VERSION_MINOR "1")
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set (SEQAN_APP_VERSION_PATCH "0")
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# don't change the following

‎src/bisulfite_scoring.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2019, Sara Hetzel <hetzel @ molgen.mpg.de>
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// Copyright (c) 2019-2024, Sara Hetzel <hetzel @ molgen.mpg.de>
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// Copyright (c) 2016-2019, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/evaluate_bisulfite_alignment.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2019, Sara Hetzel and MPI für Molekulare Genetik
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// Copyright (c) 2019-2024, Sara Hetzel and MPI für Molekulare Genetik
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// All rights reserved.
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//
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// This file is part of Lambda.

‎src/lambda.cpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/mkindex.cpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/mkindex.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/mkindex_algo.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/mkindex_misc.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/mkindex_options.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/search.cpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//
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// query file
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if (options.qryOrigAlphabet ==
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AlphabetEnum::DNA4) // means "auto", as dna4 not valid as argument to --query-alphabet
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AlphabetEnum::DNA4) // means "auto", as dna4 not valid as argument to --input-alphabet
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{
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myPrint(options, 1, "Detecting query alphabet... ");
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options.qryOrigAlphabet = detectSeqFileAlphabet(options.queryFile);

‎src/search.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/search_algo.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2019, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2019, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/search_datastructures.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/search_misc.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/search_options.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/search_output.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/shared_definitions.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/shared_misc.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//
@@ -94,8 +94,8 @@ inline AlphabetEnum detectSeqFileAlphabet(std::string const & path)
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else if (all_valid<bio::alphabet::dna15>(seq))
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{
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std::cerr << "\nWARNING: You query file was detected as non-standard DNA, but it could be AminoAcid, too.\n"
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"To explicitly read as AminoAcid, add '--query-alphabet aminoacid'.\n"
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"To ignore and disable this warning, add '--query-alphabet dna5'.\n";
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"To explicitly read as AminoAcid, add '--input-alphabet aminoacid'.\n"
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"To ignore and disable this warning, add '--input-alphabet dna5'.\n";
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return AlphabetEnum::DNA5;
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}
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else if (all_valid<bio::alphabet::aa27>(seq))

‎src/shared_options.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2013-2020, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2013-2024, Hannes Hauswedell <h2 @ fsfe.org>
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//
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// Set short description, version, and date
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parser.info.version = SEQAN_APP_VERSION;
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parser.info.date = __DATE__;
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parser.info.citation = "Hauswedell et al (2014); doi: 10.1093/bioinformatics/btu439";
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parser.info.citation = "Hauswedell & Hetzal et al (2024); doi: 10.1093/bioinformatics/btae097";
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parser.info.short_copyright =
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"2013-2020 Hannes Hauswedell, released under the GNU AGPL v3 (or later); "
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"2013-2024 Hannes Hauswedell & Sara Hetzel, released under the GNU AGPL v3 (or later); "
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"2016-2020 Knut Reinert and Freie Universität Berlin, released under the 3-clause-BSDL";
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parser.info.long_copyright =
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" Copyright (c) 2013-2020, Hannes Hauswedell\n"
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" Copyright (c) 2013-2024, Hannes Hauswedell & Sara Hetzel\n"
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" All rights reserved.\n"
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"\n"
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" This program is free software: you can redistribute it and/or modify\n"

‎src/view_dna_n_to_random.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2019, Sara Hetzel and MPI für Molekulare Genetik
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// Copyright (c) 2019-2024, Sara Hetzel and MPI für Molekulare Genetik
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/view_duplicate.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2019, Sara Hetzel and MPI für Molekulare Genetik
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// Copyright (c) 2019-2024, Sara Hetzel and MPI für Molekulare Genetik
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

‎src/view_reduce_to_bisulfite.hpp

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// ==========================================================================
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// lambda
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// ==========================================================================
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// Copyright (c) 2019, Sara Hetzel and MPI für Molekulare Genetik
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// Copyright (c) 2019-2024, Sara Hetzel and MPI für Molekulare Genetik
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// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin
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// All rights reserved.
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//

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