Added public license text to all C++ files

public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 "LoadTimeInitializer.h"
 #include "utils.h"
 using namespace std;

public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 LOAD_TIME_INITIALIZER_H
 #define LOAD_TIME_INITIALIZER_H
 #include "headers.h"

public/VectorPairHMM/src/main/c++/Makefile

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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.
+*/
+
+
 #OMPCFLAGS=-fopenmp
 #OMPLFLAGS=-fopenmp #-openmp-link static
 

public/VectorPairHMM/src/main/c++/Sandbox.cc

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 "Sandbox.h"
 #include "org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h"
 #include "utils.h"

public/VectorPairHMM/src/main/c++/Sandbox.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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.
+*/
+
+
 /* DO NOT EDIT THIS FILE - it is machine generated */
 #include <jni.h>
 /* Header for class Sandbox */

public/VectorPairHMM/src/main/c++/Sandbox.java

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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.
+*/
+
+
 import java.util.List;
 import java.util.LinkedList;
 import java.util.Map;

public/VectorPairHMM/src/main/c++/avx_function_instantiations.cc

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 "template.h"
 
 #undef SIMD_ENGINE

public/VectorPairHMM/src/main/c++/baseline.cc

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 "headers.h"
 #include "template.h"
 #include "utils.h"

public/VectorPairHMM/src/main/c++/define-double.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 <iostream>
 
 #ifdef PRECISION

public/VectorPairHMM/src/main/c++/define-float.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 <iostream>
 
 #ifdef PRECISION

public/VectorPairHMM/src/main/c++/define-sse-double.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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.
+*/
+
+
 #ifdef PRECISION
 #undef PRECISION
 #undef MAIN_TYPE

public/VectorPairHMM/src/main/c++/define-sse-float.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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.
+*/
+
+
 #ifdef PRECISION
 #undef PRECISION
 #undef MAIN_TYPE

public/VectorPairHMM/src/main/c++/headers.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 COMMON_HEADERS_H
 #define COMMON_HEADERS_H
 

public/VectorPairHMM/src/main/c++/jni_common.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 JNI_COMMON_H
 #define JNI_COMMON_H
 

public/VectorPairHMM/src/main/c++/jnidebug.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 JNI_DEBUG_H
 #define JNI_DEBUG_H
 

public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 "headers.h"
 #include "jni_common.h"
 #include "org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h"

public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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.
+*/
+
+
 /* DO NOT EDIT THIS FILE - it is machine generated */
 #include <jni.h>
 /* Header for class org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM */

public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 "headers.h"
 #include "jni_common.h"
 #include "org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h"

public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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.
+*/
+
+
 /* DO NOT EDIT THIS FILE - it is machine generated */
 #include <jni.h>
 /* Header for class org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM */

public/VectorPairHMM/src/main/c++/pairhmm-1-base.cc

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 DEBUG 1
 //#define DEBUG0_1 1
 //#define DEBUG3 1

public/VectorPairHMM/src/main/c++/pairhmm-template-kernel.cc

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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.
+*/
+
+
 #ifdef PRECISION
 
 #include <stdint.h>

public/VectorPairHMM/src/main/c++/pairhmm-template-main.cc

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 "headers.h"
 #include "template.h"
 #include "vector_defs.h"

public/VectorPairHMM/src/main/c++/shift_template.c

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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.
+*/
+
+
 #ifdef PRECISION
 
 #ifdef SIMD_ENGINE_AVX

public/VectorPairHMM/src/main/c++/sse_function_instantiations.cc

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 "template.h"
 
 #undef SIMD_ENGINE

public/VectorPairHMM/src/main/c++/template.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 TEMPLATES_H_
 #define TEMPLATES_H_
 

public/VectorPairHMM/src/main/c++/utils.cc

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 "headers.h"
 #include "template.h"
 #include "utils.h"

public/VectorPairHMM/src/main/c++/utils.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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 PAIRHMM_UTIL_H
 #define PAIRHMM_UTIL_H
 

public/VectorPairHMM/src/main/c++/vector_defs.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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.
+*/
+
+
 #undef SIMD_ENGINE
 #undef SIMD_ENGINE_AVX
 #undef SIMD_ENGINE_SSE

public/VectorPairHMM/src/main/c++/vector_function_prototypes.h

@@ -1,3 +1,28 @@
+/*Copyright (c) 2012 The Broad Institute
+
+*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.
+*/
+
+
 inline void CONCAT(CONCAT(_vector_shift,SIMD_ENGINE), PRECISION) (UNION_TYPE &x, MAIN_TYPE shiftIn, MAIN_TYPE &shiftOut);
 inline void CONCAT(CONCAT(_vector_shift_last,SIMD_ENGINE), PRECISION) (UNION_TYPE &x, MAIN_TYPE shiftIn);
 inline void CONCAT(CONCAT(precompute_masks_,SIMD_ENGINE), PRECISION)(const testcase& tc, int COLS, int numMaskVecs, MASK_TYPE (*maskArr)[NUM_DISTINCT_CHARS]);