Merge pull request #232 from h-2/prerel301

Prerel301
seqan · Aug 5, 2024 · 7512a3f · 7512a3f
2 parents 0055ca9 + 3f3bbfb
commit 7512a3f
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diff --git 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"

diff --git 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

diff --git a/src/bisulfite_scoring.hpp b/src/bisulfite_scoring.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git 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
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git a/src/mkindex.cpp b/src/mkindex.cpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git a/src/mkindex.hpp b/src/mkindex.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git a/src/mkindex_algo.hpp b/src/mkindex_algo.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git a/src/mkindex_misc.hpp b/src/mkindex_misc.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git a/src/mkindex_options.hpp b/src/mkindex_options.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git a/src/search.cpp b/src/search.cpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //
@@ -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/search.hpp b/src/search.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git a/src/search_algo.hpp b/src/search_algo.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git a/src/search_datastructures.hpp b/src/search_datastructures.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git a/src/search_misc.hpp b/src/search_misc.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git a/src/search_options.hpp b/src/search_options.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git a/src/search_output.hpp b/src/search_output.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git a/src/shared_definitions.hpp b/src/shared_definitions.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //

diff --git a/src/shared_misc.hpp b/src/shared_misc.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //
@@ -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))

diff --git a/src/shared_options.hpp b/src/shared_options.hpp
@@ -1,7 +1,7 @@
 // ==========================================================================
 //                                  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.
 //
@@ -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
@@ -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
@@ -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
@@ -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.
 //