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yuk12 committed Sep 9, 2019
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674 changes: 0 additions & 674 deletions COPYING
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43 changes: 20 additions & 23 deletions LICENSE
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GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
The MIT License

BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
Copyright (C) 2019 Vasimuddin Md, Sanchit Misra, Intel Corporation, Heng Li.

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.
BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
Copyright (C) 2019 Vasimuddin Md, Sanchit Misra, Intel Corporation, Heng Li.

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 at https://www.gnu.org/licenses/ for more details.
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.

TERMS AND CONDITIONS FOR DISTRIBUTION OF THE CODE

1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of Intel Corporation nor the names of its contributors may
be used to endorse or promote products derived from this software without
specific prior written permission.
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.

Contacts: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
Heng Li <hli@jimmy.harvard.edu>
51 changes: 24 additions & 27 deletions src/FMI_search.cpp
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/*************************************************************************************
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
Copyright (C) 2019 Vasimuddin Md, Sanchit Misra, Intel Corporation, Heng Li.
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 at https://www.gnu.org/licenses/ for more details.
TERMS AND CONDITIONS FOR DISTRIBUTION OF THE CODE
1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of Intel Corporation nor the names of its contributors may
be used to endorse or promote products derived from this software without
specific prior written permission.
The MIT License
BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
Copyright (C) 2019 Vasimuddin Md, Sanchit Misra, Intel Corporation, Heng Li.
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.
Authors: Sanchit Misra <sanchit.misra@intel.com>; Vasimuddin Md <vasimuddin.md@intel.com>;
*****************************************************************************************/
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51 changes: 24 additions & 27 deletions src/FMI_search.h
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@@ -1,31 +1,28 @@
/*************************************************************************************
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
Copyright (C) 2019 Vasimuddin Md, Sanchit Misra, Intel Corporation, Heng Li.
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 at https://www.gnu.org/licenses/ for more details.
TERMS AND CONDITIONS FOR DISTRIBUTION OF THE CODE
1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of Intel Corporation nor the names of its contributors may
be used to endorse or promote products derived from this software without
specific prior written permission.
The MIT License
BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
Copyright (C) 2019 Vasimuddin Md, Sanchit Misra, Intel Corporation, Heng Li.
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.
Authors: Sanchit Misra <sanchit.misra@intel.com>; Vasimuddin Md <vasimuddin.md@intel.com>;
*****************************************************************************************/
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51 changes: 24 additions & 27 deletions src/bandedSWA.cpp
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Original file line number Diff line number Diff line change
@@ -1,31 +1,28 @@
/*************************************************************************************
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
Copyright (C) 2019 Vasimuddin Md, Sanchit Misra, Intel Corporation, Heng Li.
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 at https://www.gnu.org/licenses/ for more details.
TERMS AND CONDITIONS FOR DISTRIBUTION OF THE CODE
1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of Intel Corporation nor the names of its contributors may
be used to endorse or promote products derived from this software without
specific prior written permission.
The MIT License
BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
Copyright (C) 2019 Vasimuddin Md, Sanchit Misra, Intel Corporation, Heng Li.
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.
Authors: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
*****************************************************************************************/
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51 changes: 24 additions & 27 deletions src/bandedSWA.h
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Original file line number Diff line number Diff line change
@@ -1,31 +1,28 @@
/*************************************************************************************
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
Copyright (C) 2019 Vasimuddin Md, Sanchit Misra, Intel Corporation, Heng Li.
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 at https://www.gnu.org/licenses/ for more details.
TERMS AND CONDITIONS FOR DISTRIBUTION OF THE CODE
1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of Intel Corporation nor the names of its contributors may
be used to endorse or promote products derived from this software without
specific prior written permission.
The MIT License
BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
Copyright (C) 2019 Vasimuddin Md, Sanchit Misra, Intel Corporation, Heng Li.
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.
Authors: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
*****************************************************************************************/
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51 changes: 24 additions & 27 deletions src/bwa.cpp
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Original file line number Diff line number Diff line change
@@ -1,31 +1,28 @@
/*************************************************************************************
GNU GENERAL PUBLIC LICENSE
Version 3, 29 June 2007
BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
Copyright (C) 2019 Vasimuddin Md, Sanchit Misra, Intel Corporation, Heng Li.
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 at https://www.gnu.org/licenses/ for more details.
TERMS AND CONDITIONS FOR DISTRIBUTION OF THE CODE
1. Redistributions of source code must retain the above copyright notice,
this list of conditions and the following disclaimer.
2. Redistributions in binary form must reproduce the above copyright notice,
this list of conditions and the following disclaimer in the documentation
and/or other materials provided with the distribution.
3. Neither the name of Intel Corporation nor the names of its contributors may
be used to endorse or promote products derived from this software without
specific prior written permission.
The MIT License
BWA-MEM2 (Sequence alignment using Burrows-Wheeler Transform),
Copyright (C) 2019 Vasimuddin Md, Sanchit Misra, Intel Corporation, Heng Li.
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.
Authors: Vasimuddin Md <vasimuddin.md@intel.com>; Sanchit Misra <sanchit.misra@intel.com>;
Heng Li <hli@jimmy.harvard.edu>
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