added MIT license to some non-GPL source files

GeoGenetics · Jul 2, 2020 · 436aceb · 436aceb
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diff --git a/bntseq.c b/bntseq.c
@@ -1,6 +1,8 @@
 /* The MIT License
 
-   Copyright (c) 2008 Genome Research Ltd (GRL).
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
 
    Permission is hereby granted, free of charge, to any person obtaining
    a copy of this software and associated documentation files (the
@@ -22,9 +24,6 @@
    CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
    SOFTWARE.
 */
-
-/* Contact: Heng Li <[email protected]> */
-
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>

diff --git a/bntseq.h b/bntseq.h
@@ -1,6 +1,8 @@
 /* The MIT License
 
-   Copyright (c) 2008 Genome Research Ltd (GRL).
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
 
    Permission is hereby granted, free of charge, to any person obtaining
    a copy of this software and associated documentation files (the
@@ -23,8 +25,6 @@
    SOFTWARE.
 */
 
-/* Contact: Heng Li <[email protected]> */
-
 #ifndef BWT_BNTSEQ_H
 #define BWT_BNTSEQ_H
 

diff --git a/bwa.c b/bwa.c
@@ -1,3 +1,29 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   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 <string.h>
 #include <stdio.h>
 #include <zlib.h>

diff --git a/bwa.h b/bwa.h
@@ -1,3 +1,29 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   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.
+*/
 #ifndef BWA_H_
 #define BWA_H_
 

diff --git a/bwamem.c b/bwamem.c
@@ -1,3 +1,29 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   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 <stdlib.h>
 #include <string.h>
 #include <stdio.h>

diff --git a/bwamem.h b/bwamem.h
@@ -1,3 +1,29 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   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.
+*/
 #ifndef BWAMEM_H_
 #define BWAMEM_H_
 

diff --git a/bwamem_extra.c b/bwamem_extra.c
@@ -1,3 +1,29 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   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 <limits.h>
 #include "bwa.h"
 #include "bwamem.h"

diff --git a/bwamem_pair.c b/bwamem_pair.c
@@ -1,3 +1,29 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   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 <stdlib.h>
 #include <string.h>
 #include <stdio.h>

diff --git a/bwt.h b/bwt.h
@@ -1,6 +1,8 @@
 /* The MIT License
 
-   Copyright (c) 2008 Genome Research Ltd (GRL).
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
 
    Permission is hereby granted, free of charge, to any person obtaining
    a copy of this software and associated documentation files (the
@@ -23,7 +25,7 @@
    SOFTWARE.
 */
 
-/* Contact: Heng Li <[email protected]> */
+/* Contact: Heng Li <[email protected]> */
 
 #ifndef BWA_BWT_H
 #define BWA_BWT_H

diff --git a/bwtindex.c b/bwtindex.c
@@ -1,6 +1,8 @@
 /* The MIT License
 
-   Copyright (c) 2008 Genome Research Ltd (GRL).
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
 
    Permission is hereby granted, free of charge, to any person obtaining
    a copy of this software and associated documentation files (the
@@ -22,9 +24,6 @@
    CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
    SOFTWARE.
 */
-
-/* Contact: Heng Li <[email protected]> */
-
 #include <stdio.h>
 #include <stdlib.h>
 #include <string.h>

diff --git a/fastmap.c b/fastmap.c
@@ -1,3 +1,29 @@
+/* The MIT License
+
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
+
+   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 <zlib.h>
 #include <stdio.h>
 #include <unistd.h>

diff --git a/utils.c b/utils.c
@@ -1,6 +1,8 @@
 /* The MIT License
 
-   Copyright (c) 2008 Genome Research Ltd (GRL).
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
 
    Permission is hereby granted, free of charge, to any person obtaining
    a copy of this software and associated documentation files (the
@@ -22,8 +24,6 @@
    CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
    SOFTWARE.
 */
-
-/* Contact: Heng Li <[email protected]> */
 #define FSYNC_ON_FLUSH
 
 #include <stdio.h>

diff --git a/utils.h b/utils.h
@@ -1,6 +1,8 @@
 /* The MIT License
 
-   Copyright (c) 2008 Genome Research Ltd (GRL).
+   Copyright (c) 2018-     Dana-Farber Cancer Institute
+                 2009-2018 Broad Institute, Inc.
+                 2008-2009 Genome Research Ltd. (GRL)
 
    Permission is hereby granted, free of charge, to any person obtaining
    a copy of this software and associated documentation files (the
@@ -22,9 +24,6 @@
    CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
    SOFTWARE.
 */
-
-/* Contact: Heng Li <[email protected]> */
-
 #ifndef LH3_UTILS_H
 #define LH3_UTILS_H