diff --git a/bntseq.c b/bntseq.c index bf67bd4..6380689 100644 --- 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 */ - #include #include #include diff --git a/bntseq.h b/bntseq.h index 03671d6..92e3afc 100644 --- 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 */ - #ifndef BWT_BNTSEQ_H #define BWT_BNTSEQ_H diff --git a/bwa.c b/bwa.c index 75ccdf4..f35b4be 100644 --- 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 #include #include diff --git a/bwa.h b/bwa.h index aa21725..9668950 100644 --- 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 index deb56d6..966e8d0 100644 --- 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 #include #include diff --git a/bwamem.h b/bwamem.h index fe537fa..0a0e3bb 100644 --- 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 index fb42abd..0d64e79 100644 --- 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 #include "bwa.h" #include "bwamem.h" diff --git a/bwamem_pair.c b/bwamem_pair.c index 9beb84b..ef79521 100644 --- 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 #include #include diff --git a/bwt.h b/bwt.h index c71d6b5..daba87f 100644 --- 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 */ +/* Contact: Heng Li */ #ifndef BWA_BWT_H #define BWA_BWT_H diff --git a/bwtindex.c b/bwtindex.c index e1322f8..6a27ae1 100644 --- 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 */ - #include #include #include diff --git a/fastmap.c b/fastmap.c index 53d2b71..c865426 100644 --- 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 #include #include diff --git a/utils.c b/utils.c index 2983261..21d5281 100644 --- 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 */ #define FSYNC_ON_FLUSH #include diff --git a/utils.h b/utils.h index 11966b8..9d80784 100644 --- 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 */ - #ifndef LH3_UTILS_H #define LH3_UTILS_H