Update copyrights in all C++ source files

joepickrell · Apr 11, 2020 · 62bda67 · 62bda67
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diff --git a/chunk/src/chunk.cpp b/chunk/src/chunk.cpp
@@ -1,3 +1,26 @@
+/*******************************************************************************
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
+
 #define _DECLARE_TOOLBOX_HERE
 #include <chunker/chunker_header.h>
 

diff --git a/chunk/src/chunker/chunker_algorithm.cpp b/chunk/src/chunker/chunker_algorithm.cpp
@@ -1,24 +1,26 @@
-////////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 2018 Olivier Delaneau, University of Lausanne
-// 
-// Permission is hereby granted, free of charge, to any person obtaining a copy
-// of this software and associated documentation files (the "Software"), to deal
-// in the Software without restriction, including without limitation the rights
-// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-// copies of the Software, and to permit persons to whom the Software is
-// furnished to do so, subject to the following conditions:
-// 
-// The above copyright notice and this permission notice shall be included in
-// all copies or substantial portions of the Software.
-// 
-// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-// SOFTWARE.
-////////////////////////////////////////////////////////////////////////////////
+/*******************************************************************************
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
+
 #include <chunker/chunker_header.h>
 
 void chunker::split(output_file & fd, int & cidx, string & chr, int start_idx, int stop_idx) {

diff --git a/chunk/src/chunker/chunker_header.h b/chunk/src/chunker/chunker_header.h
@@ -1,5 +1,6 @@
 /*******************************************************************************
- * Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
  * 
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal

diff --git a/chunk/src/chunker/chunker_io.cpp b/chunk/src/chunker/chunker_io.cpp
@@ -1,24 +1,26 @@
-////////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 2018 Olivier Delaneau, University of Lausanne
-// 
-// Permission is hereby granted, free of charge, to any person obtaining a copy
-// of this software and associated documentation files (the "Software"), to deal
-// in the Software without restriction, including without limitation the rights
-// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-// copies of the Software, and to permit persons to whom the Software is
-// furnished to do so, subject to the following conditions:
-// 
-// The above copyright notice and this permission notice shall be included in
-// all copies or substantial portions of the Software.
-// 
-// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-// SOFTWARE.
-////////////////////////////////////////////////////////////////////////////////
+/*******************************************************************************
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
+
 #include <chunker/chunker_header.h>
 
 void chunker::readData(string fmain, string freference, string region) {

diff --git a/chunk/src/chunker/chunker_management.cpp b/chunk/src/chunker/chunker_management.cpp
@@ -1,24 +1,26 @@
-////////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 2018 Olivier Delaneau, University of Lausanne
-// 
-// Permission is hereby granted, free of charge, to any person obtaining a copy
-// of this software and associated documentation files (the "Software"), to deal
-// in the Software without restriction, including without limitation the rights
-// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-// copies of the Software, and to permit persons to whom the Software is
-// furnished to do so, subject to the following conditions:
-// 
-// The above copyright notice and this permission notice shall be included in
-// all copies or substantial portions of the Software.
-// 
-// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-// SOFTWARE.
-////////////////////////////////////////////////////////////////////////////////
+/*******************************************************************************
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
+
 #include <chunker/chunker_header.h>
 
 chunker::chunker() {

diff --git a/chunk/src/chunker/chunker_parameters.cpp b/chunk/src/chunker/chunker_parameters.cpp
@@ -1,24 +1,25 @@
-////////////////////////////////////////////////////////////////////////////////
-// Copyright (C) 2018 Olivier Delaneau, University of Lausanne
-// 
-// Permission is hereby granted, free of charge, to any person obtaining a copy
-// of this software and associated documentation files (the "Software"), to deal
-// in the Software without restriction, including without limitation the rights
-// to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
-// copies of the Software, and to permit persons to whom the Software is
-// furnished to do so, subject to the following conditions:
-// 
-// The above copyright notice and this permission notice shall be included in
-// all copies or substantial portions of the Software.
-// 
-// THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
-// IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
-// FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
-// AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
-// LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
-// OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
-// SOFTWARE.
-////////////////////////////////////////////////////////////////////////////////
+/*******************************************************************************
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
+ *
+ * Permission is hereby granted, free of charge, to any person obtaining a copy
+ * of this software and associated documentation files (the "Software"), to deal
+ * in the Software without restriction, including without limitation the rights
+ * to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
+ * copies of the Software, and to permit persons to whom the Software is
+ * furnished to do so, subject to the following conditions:
+ *
+ * The above copyright notice and this permission notice shall be included in
+ * all copies or substantial portions of the Software.
+ *
+ * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
+ * IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
+ * FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
+ * AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
+ * LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
+ * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
+ * SOFTWARE.
+ ******************************************************************************/
 
 #include "../../versions/versions.h"
 #include <chunker/chunker_header.h>

diff --git a/chunk/src/utils/basic_algos.h b/chunk/src/utils/basic_algos.h
@@ -1,5 +1,6 @@
 /*******************************************************************************
- * Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
  * 
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -19,6 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
  ******************************************************************************/
+
 #ifndef _BASIC_ALGOS_H
 #define _BASIC_ALGOS_H
 

diff --git a/chunk/src/utils/basic_stats.h b/chunk/src/utils/basic_stats.h
@@ -1,5 +1,6 @@
 /*******************************************************************************
- * Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
  * 
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -19,6 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
  ******************************************************************************/
+
 #ifndef _BASIC_STATS_H
 #define _BASIC_STATS_H
 

diff --git a/chunk/src/utils/compressed_io.h b/chunk/src/utils/compressed_io.h
@@ -1,5 +1,6 @@
 /*******************************************************************************
- * Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
  * 
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -19,6 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
  ******************************************************************************/
+
 #ifndef _COMPRESSED_IO_H
 #define _COMPRESSED_IO_H
 

diff --git a/chunk/src/utils/otools.h b/chunk/src/utils/otools.h
@@ -1,5 +1,6 @@
 /*******************************************************************************
- * Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
  * 
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -19,6 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
  ******************************************************************************/
+
 #ifndef _OLIVIER_TOOLS_H
 #define _OLIVIER_TOOLS_H
 

diff --git a/chunk/src/utils/random_number.h b/chunk/src/utils/random_number.h
@@ -1,5 +1,6 @@
 /*******************************************************************************
- * Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
  * 
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -19,6 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
  ******************************************************************************/
+
 #ifndef _RANDOM_NUMBER_H
 #define _RANDOM_NUMBER_H
 

diff --git a/chunk/src/utils/string_utils.h b/chunk/src/utils/string_utils.h
@@ -1,5 +1,6 @@
 /*******************************************************************************
- * Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
  * 
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -19,6 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
  ******************************************************************************/
+
 #ifndef _STRING_UTILS_H
 #define _STRING_UTILS_H
 

diff --git a/chunk/src/utils/timer.h b/chunk/src/utils/timer.h
@@ -1,5 +1,6 @@
 /*******************************************************************************
- * Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
  * 
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -19,6 +20,7 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
  ******************************************************************************/
+
 #ifndef _TIMER_H
 #define _TIMER_H
 

diff --git a/chunk/src/utils/verbose.h b/chunk/src/utils/verbose.h
@@ -1,5 +1,6 @@
 /*******************************************************************************
- * Copyright (C) 2018 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Olivier Delaneau, University of Lausanne
+ * Copyright (C) 2020 Simone Rubinacci, University of Lausanne
  * 
  * Permission is hereby granted, free of charge, to any person obtaining a copy
  * of this software and associated documentation files (the "Software"), to deal
@@ -19,20 +20,6 @@
  * OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
  * SOFTWARE.
  ******************************************************************************/
-/*Copyright (C) 2015 Olivier Delaneau, University of Lausanne, Halit Ongen, Emmanouil T. Dermitzakis
- 
- This program is free software: you can redistribute it and/or modify
- it under the terms of the GNU General Public License as published by
- the Free Software Foundation, either version 3 of the License, or
- (at your option) any later version.
- 
- This program is distributed in the hope that it will be useful,
- but WITHOUT ANY WARRANTY; without even the implied warranty of
- MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
- GNU General Public License for more details.
- 
- You should have received a copy of the GNU General Public License
- along with this program.  If not, see <http://www.gnu.org/licenses/>.*/
 
 #ifndef _VERBOSE_H
 #define _VERBOSE_H