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"