update all copyrights

ablab · Mar 18, 2024 · 2e2ba6e · 2e2ba6e
1 parent 97c29a2
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diff --git a/make-targz.sh b/make-targz.sh
@@ -1,3 +1,10 @@
+
+############################################################################
+# Copyright (c) 2023-2024 SPAdes team
+# All Rights Reserved
+# See file LICENSE for details.
+############################################################################
+
 VERSION="$(cat assembler/VERSION)"
 : "${TARGET_DIR:=SPAdes-$VERSION}"
 rm -rf $TARGET_DIR

diff --git a/spades_compile.sh b/spades_compile.sh
@@ -1,7 +1,8 @@
 #!/bin/bash
 
 ############################################################################
-# Copyright (c) 2015-2020 Saint Petersburg State University
+# Copyright (c) 2023-2024 SPAdes team
+# Copyright (c) 2015-2022 Saint Petersburg State University
 # Copyright (c) 2011-2014 Saint Petersburg Academic University
 # All Rights Reserved
 # See file LICENSE for details.

diff --git a/src/CMakeLists.txt b/src/CMakeLists.txt
@@ -1,6 +1,7 @@
 # -*- cmake -*-
 ############################################################################
-# Copyright (c) 2015 Saint Petersburg State University
+# Copyright (c) 2023-2024 SPAdes team
+# Copyright (c) 2015-2022 Saint Petersburg State University
 # Copyright (c) 2011-2014 Saint Petersburg Academic University
 # All Rights Reserved
 # See file LICENSE for details.

diff --git a/src/CMakeListsInternal.txt b/src/CMakeListsInternal.txt
@@ -1,5 +1,6 @@
 ############################################################################
-# Copyright (c) 2015 Saint Petersburg State University
+# Copyright (c) 2023-2024 SPAdes team
+# Copyright (c) 2015-2022 Saint Petersburg State University
 # Copyright (c) 2011-2014 Saint Petersburg Academic University
 # All Rights Reserved
 # See file LICENSE for details.

diff --git a/src/common/CMakeLists.txt b/src/common/CMakeLists.txt
@@ -1,5 +1,6 @@
 ############################################################################
-# Copyright (c) 2015 Saint Petersburg State University
+# Copyright (c) 2023-2024 SPAdes team
+# Copyright (c) 2015-2022 Saint Petersburg State University
 # Copyright (c) 2011-2014 Saint Petersburg Academic University
 # All Rights Reserved
 # See file LICENSE for details.

diff --git a/src/common/adt/array_vector.hpp b/src/common/adt/array_vector.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* Copyright (c) 2011-2014 Saint Petersburg Academic University
 //* All Rights Reserved
 //* See file LICENSE for details.

diff --git a/src/common/adt/bag.hpp b/src/common/adt/bag.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* Copyright (c) 2011-2014 Saint Petersburg Academic University
 //* All Rights Reserved
 //* See file LICENSE for details.

diff --git a/src/common/adt/bf.hpp b/src/common/adt/bf.hpp
@@ -1,3 +1,10 @@
+
+//***************************************************************************
+//* Copyright (c) 2023-2024 SPAdes team
+//* All Rights Reserved
+//* See file LICENSE for details.
+//***************************************************************************
+
 #pragma once
 
 #include "lemiere_mod_reduce.hpp"

diff --git a/src/common/adt/chained_iterator.hpp b/src/common/adt/chained_iterator.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* Copyright (c) 2011-2014 Saint Petersburg Academic University
 //* All Rights Reserved
 //* See file LICENSE for details.

diff --git a/src/common/adt/concurrent_dsu.cpp b/src/common/adt/concurrent_dsu.cpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2019 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2019-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/adt/concurrent_dsu.hpp b/src/common/adt/concurrent_dsu.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* Copyright (c) 2011-2014 Saint Petersburg Academic University
 //* All Rights Reserved
 //* See file LICENSE for details.

diff --git a/src/common/adt/cqf.hpp b/src/common/adt/cqf.hpp
@@ -1,3 +1,10 @@
+
+//***************************************************************************
+//* Copyright (c) 2023-2024 SPAdes team
+//* All Rights Reserved
+//* See file LICENSE for details.
+//***************************************************************************
+
 #pragma once
 
 #include "gqf/gqf.h"

diff --git a/src/common/adt/cyclichash.hpp b/src/common/adt/cyclichash.hpp
@@ -1,3 +1,10 @@
+
+//***************************************************************************
+//* Copyright (c) 2023-2024 SPAdes team
+//* All Rights Reserved
+//* See file LICENSE for details.
+//***************************************************************************
+
 #pragma once
 
 #include "sequence/nucl.hpp"

diff --git a/src/common/adt/filter_iterator.hpp b/src/common/adt/filter_iterator.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* Copyright (c) 2011-2014 Saint Petersburg Academic University
 //* All Rights Reserved
 //* See file LICENSE for details.

diff --git a/src/common/adt/flat_map.hpp b/src/common/adt/flat_map.hpp
@@ -1,3 +1,10 @@
+
+//***************************************************************************
+//* Copyright (c) 2023-2024 SPAdes team
+//* All Rights Reserved
+//* See file LICENSE for details.
+//***************************************************************************
+
 #ifndef __ADT_FLAT_MAP_HPP__
 #define __ADT_FLAT_MAP_HPP__
 

diff --git a/src/common/adt/flat_set.hpp b/src/common/adt/flat_set.hpp
@@ -1,3 +1,10 @@
+
+//***************************************************************************
+//* Copyright (c) 2023-2024 SPAdes team
+//* All Rights Reserved
+//* See file LICENSE for details.
+//***************************************************************************
+
 #ifndef __ADT_FLAT_SET_HPP__
 #define __ADT_FLAT_SET_HPP__
 

diff --git a/src/common/adt/hll.hpp b/src/common/adt/hll.hpp
@@ -1,3 +1,10 @@
+
+//***************************************************************************
+//* Copyright (c) 2023-2024 SPAdes team
+//* All Rights Reserved
+//* See file LICENSE for details.
+//***************************************************************************
+
 #pragma once
 
 #include <vector>

diff --git a/src/common/adt/iterator_range.hpp b/src/common/adt/iterator_range.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/adt/kmer_vector.hpp b/src/common/adt/kmer_vector.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* Copyright (c) 2011-2014 Saint Petersburg Academic University
 //* All Rights Reserved
 //* See file LICENSE for details.

diff --git a/src/common/adt/lemiere_mod_reduce.hpp b/src/common/adt/lemiere_mod_reduce.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2020 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2020-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/adt/loser_tree.hpp b/src/common/adt/loser_tree.hpp
@@ -1,3 +1,10 @@
+
+//***************************************************************************
+//* Copyright (c) 2023-2024 SPAdes team
+//* All Rights Reserved
+//* See file LICENSE for details.
+//***************************************************************************
+
 #pragma once
 
 #include "iterator_range.hpp"

diff --git a/src/common/adt/pack.hpp b/src/common/adt/pack.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2018 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2018-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/adt/pointer_iterator.hpp b/src/common/adt/pointer_iterator.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* Copyright (c) 2011-2014 Saint Petersburg Academic University
 //* All Rights Reserved
 //* See file LICENSE for details.

diff --git a/src/common/adt/queue_iterator.hpp b/src/common/adt/queue_iterator.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* Copyright (c) 2011-2014 Saint Petersburg Academic University
 //* All Rights Reserved
 //* See file LICENSE for details.

diff --git a/src/common/adt/small_pod_vector.hpp b/src/common/adt/small_pod_vector.hpp
@@ -1,3 +1,10 @@
+
+//***************************************************************************
+//* Copyright (c) 2023-2024 SPAdes team
+//* All Rights Reserved
+//* See file LICENSE for details.
+//***************************************************************************
+
 #ifndef __ADT_SMALL_POD_VECTOR__
 #define __ADT_SMALL_POD_VECTOR__
 

diff --git a/src/common/alignment/CMakeLists.txt b/src/common/alignment/CMakeLists.txt
@@ -1,5 +1,6 @@
 ############################################################################
-# Copyright (c) 2015 Saint Petersburg State University
+# Copyright (c) 2023-2024 SPAdes team
+# Copyright (c) 2015-2022 Saint Petersburg State University
 # Copyright (c) 2011-2014 Saint Petersburg Academic University
 # All Rights Reserved
 # See file LICENSE for details.

diff --git a/src/common/alignment/bwa_index.cpp b/src/common/alignment/bwa_index.cpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2016 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2016-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/alignment/bwa_index.hpp b/src/common/alignment/bwa_index.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2016 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2016-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/alignment/bwa_sequence_mapper.hpp b/src/common/alignment/bwa_sequence_mapper.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2016 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2016-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/alignment/edge_index.hpp b/src/common/alignment/edge_index.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* Copyright (c) 2011-2014 Saint Petersburg Academic University
 //* All Rights Reserved
 //* See file LICENSE for details.

diff --git a/src/common/alignment/edge_index_refiller.cpp b/src/common/alignment/edge_index_refiller.cpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2016 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2016-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/alignment/edge_index_refiller.hpp b/src/common/alignment/edge_index_refiller.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2016 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2016-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/alignment/gap_info.cpp b/src/common/alignment/gap_info.cpp
@@ -1,3 +1,10 @@
+
+//***************************************************************************
+//* Copyright (c) 2023-2024 SPAdes team
+//* All Rights Reserved
+//* See file LICENSE for details.
+//***************************************************************************
+
 #include "gap_info.hpp"
 
 #include "io/reads/single_read.hpp"

diff --git a/src/common/alignment/gap_info.hpp b/src/common/alignment/gap_info.hpp
@@ -1,3 +1,10 @@
+
+//***************************************************************************
+//* Copyright (c) 2023-2024 SPAdes team
+//* All Rights Reserved
+//* See file LICENSE for details.
+//***************************************************************************
+
 #pragma once
 
 #include "sequence/sequence.hpp"

diff --git a/src/common/alignment/kmer_map.hpp b/src/common/alignment/kmer_map.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2016 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2016-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/alignment/kmer_mapper.hpp b/src/common/alignment/kmer_mapper.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* Copyright (c) 2011-2014 Saint Petersburg Academic University
 //* All Rights Reserved
 //* See file LICENSE for details.

diff --git a/src/common/alignment/kmer_mapper_logger.hpp b/src/common/alignment/kmer_mapper_logger.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* Copyright (c) 2011-2014 Saint Petersburg Academic University
 //* All Rights Reserved
 //* See file LICENSE for details.

diff --git a/src/common/alignment/kmer_sequence_mapper.cpp b/src/common/alignment/kmer_sequence_mapper.cpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2021 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2021-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/alignment/kmer_sequence_mapper.hpp b/src/common/alignment/kmer_sequence_mapper.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2021 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2021-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/alignment/long_read_mapper.cpp b/src/common/alignment/long_read_mapper.cpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2020 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2020-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/alignment/long_read_mapper.hpp b/src/common/alignment/long_read_mapper.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* Copyright (c) 2011-2014 Saint Petersburg Academic University
 //* All Rights Reserved
 //* See file LICENSE for details.

diff --git a/src/common/alignment/long_read_storage.hpp b/src/common/alignment/long_read_storage.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* Copyright (c) 2011-2014 Saint Petersburg Academic University
 //* All Rights Reserved
 //* See file LICENSE for details.

diff --git a/src/common/alignment/pacbio/g_aligner.cpp b/src/common/alignment/pacbio/g_aligner.cpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015-2019 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/alignment/pacbio/g_aligner.hpp b/src/common/alignment/pacbio/g_aligner.hpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2015-2019 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2015-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************

diff --git a/src/common/alignment/pacbio/gap_dijkstra.cpp b/src/common/alignment/pacbio/gap_dijkstra.cpp
@@ -1,5 +1,6 @@
 //***************************************************************************
-//* Copyright (c) 2018 Saint Petersburg State University
+//* Copyright (c) 2023-2024 SPAdes team
+//* Copyright (c) 2018-2022 Saint Petersburg State University
 //* All Rights Reserved
 //* See file LICENSE for details.
 //***************************************************************************