From e678917577ce7966f4bdad5db06a5940c8c76e82 Mon Sep 17 00:00:00 2001 From: Hannes Hauswedell Date: Sun, 4 Aug 2024 17:44:42 +0100 Subject: [PATCH 1/4] [misc] bump version --- src/CMakeLists.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt index c05ce5675..45ddb9fa4 100644 --- a/src/CMakeLists.txt +++ b/src/CMakeLists.txt @@ -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 From 6ac098fb2eb43f71a5e44a4226ea1242f8e025e2 Mon Sep 17 00:00:00 2001 From: Hannes Hauswedell Date: Sun, 4 Aug 2024 17:48:29 +0100 Subject: [PATCH 2/4] [misc] update citation and copyright --- src/bisulfite_scoring.hpp | 2 +- src/evaluate_bisulfite_alignment.hpp | 2 +- src/lambda.cpp | 2 +- src/mkindex.cpp | 2 +- src/mkindex.hpp | 2 +- src/mkindex_algo.hpp | 2 +- src/mkindex_misc.hpp | 2 +- src/mkindex_options.hpp | 2 +- src/search.cpp | 2 +- src/search.hpp | 2 +- src/search_algo.hpp | 2 +- src/search_datastructures.hpp | 2 +- src/search_misc.hpp | 2 +- src/search_options.hpp | 2 +- src/search_output.hpp | 2 +- src/shared_definitions.hpp | 2 +- src/shared_misc.hpp | 2 +- src/shared_options.hpp | 8 ++++---- src/view_dna_n_to_random.hpp | 2 +- src/view_duplicate.hpp | 2 +- src/view_reduce_to_bisulfite.hpp | 2 +- 21 files changed, 24 insertions(+), 24 deletions(-) diff --git a/src/bisulfite_scoring.hpp b/src/bisulfite_scoring.hpp index 2dac932d0..743506291 100644 --- a/src/bisulfite_scoring.hpp +++ b/src/bisulfite_scoring.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2019, Sara Hetzel +// Copyright (c) 2019-2024, Sara Hetzel // Copyright (c) 2016-2019, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/evaluate_bisulfite_alignment.hpp b/src/evaluate_bisulfite_alignment.hpp index c38ad46fa..b9a272545 100644 --- a/src/evaluate_bisulfite_alignment.hpp +++ b/src/evaluate_bisulfite_alignment.hpp @@ -1,7 +1,7 @@ // ========================================================================== // 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. diff --git a/src/lambda.cpp b/src/lambda.cpp index 365ddb2e7..77be0b4c3 100644 --- a/src/lambda.cpp +++ b/src/lambda.cpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/mkindex.cpp b/src/mkindex.cpp index 566e61036..345ecbda3 100644 --- a/src/mkindex.cpp +++ b/src/mkindex.cpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/mkindex.hpp b/src/mkindex.hpp index fbb2bd872..9005fce66 100644 --- a/src/mkindex.hpp +++ b/src/mkindex.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/mkindex_algo.hpp b/src/mkindex_algo.hpp index c26851889..8bc7ca00c 100644 --- a/src/mkindex_algo.hpp +++ b/src/mkindex_algo.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/mkindex_misc.hpp b/src/mkindex_misc.hpp index 0b25ac136..144574d40 100644 --- a/src/mkindex_misc.hpp +++ b/src/mkindex_misc.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/mkindex_options.hpp b/src/mkindex_options.hpp index 66074b7df..484d548a1 100644 --- a/src/mkindex_options.hpp +++ b/src/mkindex_options.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/search.cpp b/src/search.cpp index b01b504b1..171724b66 100644 --- a/src/search.cpp +++ b/src/search.cpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/search.hpp b/src/search.hpp index 62c6d8365..27a4b551d 100644 --- a/src/search.hpp +++ b/src/search.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/search_algo.hpp b/src/search_algo.hpp index ffe259643..09bdd0b75 100644 --- a/src/search_algo.hpp +++ b/src/search_algo.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2019, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2019, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/search_datastructures.hpp b/src/search_datastructures.hpp index f606d95e3..1d4499ee5 100644 --- a/src/search_datastructures.hpp +++ b/src/search_datastructures.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/search_misc.hpp b/src/search_misc.hpp index d0d92dfeb..805c8be2c 100644 --- a/src/search_misc.hpp +++ b/src/search_misc.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/search_options.hpp b/src/search_options.hpp index 7d7589cfb..dc347e64e 100644 --- a/src/search_options.hpp +++ b/src/search_options.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/search_output.hpp b/src/search_output.hpp index c9181c437..adcc7478c 100644 --- a/src/search_output.hpp +++ b/src/search_output.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/shared_definitions.hpp b/src/shared_definitions.hpp index b56db1945..28784fb6b 100644 --- a/src/shared_definitions.hpp +++ b/src/shared_definitions.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/shared_misc.hpp b/src/shared_misc.hpp index 1ee56aaa6..7211a6908 100644 --- a/src/shared_misc.hpp +++ b/src/shared_misc.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // diff --git a/src/shared_options.hpp b/src/shared_options.hpp index 23780ce34..06e2533f1 100644 --- a/src/shared_options.hpp +++ b/src/shared_options.hpp @@ -1,7 +1,7 @@ // ========================================================================== // lambda // ========================================================================== -// Copyright (c) 2013-2020, Hannes Hauswedell

+// Copyright (c) 2013-2024, Hannes Hauswedell

// Copyright (c) 2016-2020, Knut Reinert and Freie Universität Berlin // All rights reserved. // @@ -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" diff --git a/src/view_dna_n_to_random.hpp b/src/view_dna_n_to_random.hpp index 82cadbd4d..630685bc1 100644 --- a/src/view_dna_n_to_random.hpp +++ b/src/view_dna_n_to_random.hpp @@ -1,7 +1,7 @@ // ========================================================================== // 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. // diff --git a/src/view_duplicate.hpp b/src/view_duplicate.hpp index c4dc7d4ab..4612e89ac 100644 --- a/src/view_duplicate.hpp +++ b/src/view_duplicate.hpp @@ -1,7 +1,7 @@ // ========================================================================== // 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. // diff --git a/src/view_reduce_to_bisulfite.hpp b/src/view_reduce_to_bisulfite.hpp index 19062e0c3..b540767f8 100644 --- a/src/view_reduce_to_bisulfite.hpp +++ b/src/view_reduce_to_bisulfite.hpp @@ -1,7 +1,7 @@ // ========================================================================== // 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. // From 6b9ffa0311a9e9c756353e0021d89c3cb5e9690c Mon Sep 17 00:00:00 2001 From: Hannes Hauswedell Date: Sun, 4 Aug 2024 17:52:12 +0100 Subject: [PATCH 3/4] [doc] fix documentation for --input-alphabet --- src/search.cpp | 2 +- src/shared_misc.hpp | 4 ++-- 2 files changed, 3 insertions(+), 3 deletions(-) diff --git a/src/search.cpp b/src/search.cpp index 171724b66..38742cf74 100644 --- a/src/search.cpp +++ b/src/search.cpp @@ -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); diff --git a/src/shared_misc.hpp b/src/shared_misc.hpp index 7211a6908..573d65e1a 100644 --- a/src/shared_misc.hpp +++ b/src/shared_misc.hpp @@ -94,8 +94,8 @@ inline AlphabetEnum detectSeqFileAlphabet(std::string const & path) else if (all_valid(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(seq)) From 3f3bbfb3f5bcc80a836bd101bfa168509622fa62 Mon Sep 17 00:00:00 2001 From: Hannes Hauswedell Date: Mon, 5 Aug 2024 18:45:19 +0100 Subject: [PATCH 4/4] [ci] update macos runner to -13 --- .github/workflows/ci_macos.yml | 8 ++++---- 1 file changed, 4 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci_macos.yml b/.github/workflows/ci_macos.yml index 7264e46e6..78a70b013 100644 --- a/.github/workflows/ci_macos.yml +++ b/.github/workflows/ci_macos.yml @@ -16,15 +16,15 @@ defaults: jobs: build: name: ${{ matrix.name }} - runs-on: macos-11 + runs-on: macos-13 timeout-minutes: 120 strategy: fail-fast: false matrix: include: - - name: "gcc13" - cxx: "g++-13" - cc: "gcc-13" + - name: "gcc12" + cxx: "g++-12" + cc: "gcc-12" build_type: Release - name: "gcc11"