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added MIT license to some non-GPL source files

This commit is contained in:
Heng Li 2020-07-01 23:02:01 -04:00
parent 3a2b0c05dd
commit 436aceb4ef
13 changed files with 201 additions and 20 deletions
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7
bntseq.c
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@ -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 <lh3@sanger.ac.uk> */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>

6
bntseq.h
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@ -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 <lh3@sanger.ac.uk> */
#ifndef BWT_BNTSEQ_H
#define BWT_BNTSEQ_H

26
bwa.c
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@ -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>

26
bwa.h
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@ -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_

26
bwamem.c
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@ -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>

26
bwamem.h
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@ -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_

26
bwamem_extra.c
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@ -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"

26
bwamem_pair.c
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@ -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>

6
bwt.h
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@ -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 <lh3@sanger.ac.uk> */
/* Contact: Heng Li <hli@jimmy.harvard.edu> */
#ifndef BWA_BWT_H
#define BWA_BWT_H

7
bwtindex.c
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@ -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 <lh3@sanger.ac.uk> */
#include <stdio.h>
#include <stdlib.h>
#include <string.h>

26
fastmap.c
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@ -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>

6
utils.c
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@ -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 <lh3@sanger.ac.uk> */
#define FSYNC_ON_FLUSH
#include <stdio.h>

7
utils.h
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@ -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 <lh3@sanger.ac.uk> */
#ifndef LH3_UTILS_H
#define LH3_UTILS_H