From 7cd23543a1d7ddd067ac8c673757c8a67277b44e Mon Sep 17 00:00:00 2001 From: Karthik Gururaj Date: Mon, 3 Mar 2014 09:04:00 -0800 Subject: [PATCH] Added public license text to all C++ files --- .../src/main/c++/LoadTimeInitializer.cc | 25 +++++++++++++++++++ .../src/main/c++/LoadTimeInitializer.h | 25 +++++++++++++++++++ public/VectorPairHMM/src/main/c++/Makefile | 25 +++++++++++++++++++ public/VectorPairHMM/src/main/c++/Sandbox.cc | 25 +++++++++++++++++++ public/VectorPairHMM/src/main/c++/Sandbox.h | 25 +++++++++++++++++++ .../VectorPairHMM/src/main/c++/Sandbox.java | 25 +++++++++++++++++++ .../main/c++/avx_function_instantiations.cc | 25 +++++++++++++++++++ public/VectorPairHMM/src/main/c++/baseline.cc | 25 +++++++++++++++++++ .../src/main/c++/define-double.h | 25 +++++++++++++++++++ .../VectorPairHMM/src/main/c++/define-float.h | 25 +++++++++++++++++++ .../src/main/c++/define-sse-double.h | 25 +++++++++++++++++++ .../src/main/c++/define-sse-float.h | 25 +++++++++++++++++++ public/VectorPairHMM/src/main/c++/headers.h | 25 +++++++++++++++++++ .../VectorPairHMM/src/main/c++/jni_common.h | 25 +++++++++++++++++++ public/VectorPairHMM/src/main/c++/jnidebug.h | 25 +++++++++++++++++++ ...ng_utils_pairhmm_DebugJNILoglessPairHMM.cc | 25 +++++++++++++++++++ ...ing_utils_pairhmm_DebugJNILoglessPairHMM.h | 25 +++++++++++++++++++ ...ting_utils_pairhmm_VectorLoglessPairHMM.cc | 25 +++++++++++++++++++ ...sting_utils_pairhmm_VectorLoglessPairHMM.h | 25 +++++++++++++++++++ .../src/main/c++/pairhmm-1-base.cc | 25 +++++++++++++++++++ .../src/main/c++/pairhmm-template-kernel.cc | 25 +++++++++++++++++++ .../src/main/c++/pairhmm-template-main.cc | 25 +++++++++++++++++++ .../src/main/c++/shift_template.c | 25 +++++++++++++++++++ .../main/c++/sse_function_instantiations.cc | 25 +++++++++++++++++++ public/VectorPairHMM/src/main/c++/template.h | 25 +++++++++++++++++++ public/VectorPairHMM/src/main/c++/utils.cc | 25 +++++++++++++++++++ public/VectorPairHMM/src/main/c++/utils.h | 25 +++++++++++++++++++ .../VectorPairHMM/src/main/c++/vector_defs.h | 25 +++++++++++++++++++ .../src/main/c++/vector_function_prototypes.h | 25 +++++++++++++++++++ 29 files changed, 725 insertions(+) diff --git a/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc b/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc index 3aacefe72..0e3026f65 100644 --- a/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.cc +++ b/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; diff --git a/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h b/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h index 1834405a5..e7d9af626 100644 --- a/public/VectorPairHMM/src/main/c++/LoadTimeInitializer.h +++ b/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" diff --git a/public/VectorPairHMM/src/main/c++/Makefile b/public/VectorPairHMM/src/main/c++/Makefile index da91149e9..7296b7026 100644 --- a/public/VectorPairHMM/src/main/c++/Makefile +++ b/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 diff --git a/public/VectorPairHMM/src/main/c++/Sandbox.cc b/public/VectorPairHMM/src/main/c++/Sandbox.cc index 8fb0d0b67..985b19ae9 100644 --- a/public/VectorPairHMM/src/main/c++/Sandbox.cc +++ b/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" diff --git a/public/VectorPairHMM/src/main/c++/Sandbox.h b/public/VectorPairHMM/src/main/c++/Sandbox.h index 4ac1ea24c..486a1c095 100644 --- a/public/VectorPairHMM/src/main/c++/Sandbox.h +++ b/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 /* Header for class Sandbox */ diff --git a/public/VectorPairHMM/src/main/c++/Sandbox.java b/public/VectorPairHMM/src/main/c++/Sandbox.java index 81a57c0a0..ee55ccbac 100644 --- a/public/VectorPairHMM/src/main/c++/Sandbox.java +++ b/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; diff --git a/public/VectorPairHMM/src/main/c++/avx_function_instantiations.cc b/public/VectorPairHMM/src/main/c++/avx_function_instantiations.cc index 8f0de827d..6d90d5070 100644 --- a/public/VectorPairHMM/src/main/c++/avx_function_instantiations.cc +++ b/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 diff --git a/public/VectorPairHMM/src/main/c++/baseline.cc b/public/VectorPairHMM/src/main/c++/baseline.cc index 66aeacbc4..d6085e661 100644 --- a/public/VectorPairHMM/src/main/c++/baseline.cc +++ b/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" diff --git a/public/VectorPairHMM/src/main/c++/define-double.h b/public/VectorPairHMM/src/main/c++/define-double.h index 83589a13d..2067d369c 100644 --- a/public/VectorPairHMM/src/main/c++/define-double.h +++ b/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 #ifdef PRECISION diff --git a/public/VectorPairHMM/src/main/c++/define-float.h b/public/VectorPairHMM/src/main/c++/define-float.h index 87b2b01f3..318f78280 100644 --- a/public/VectorPairHMM/src/main/c++/define-float.h +++ b/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 #ifdef PRECISION diff --git a/public/VectorPairHMM/src/main/c++/define-sse-double.h b/public/VectorPairHMM/src/main/c++/define-sse-double.h index d781d55f3..2d271a854 100644 --- a/public/VectorPairHMM/src/main/c++/define-sse-double.h +++ b/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 diff --git a/public/VectorPairHMM/src/main/c++/define-sse-float.h b/public/VectorPairHMM/src/main/c++/define-sse-float.h index 7516e6dbf..20af947dd 100644 --- a/public/VectorPairHMM/src/main/c++/define-sse-float.h +++ b/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 diff --git a/public/VectorPairHMM/src/main/c++/headers.h b/public/VectorPairHMM/src/main/c++/headers.h index 48bd4d836..4a0d89b57 100644 --- a/public/VectorPairHMM/src/main/c++/headers.h +++ b/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 diff --git a/public/VectorPairHMM/src/main/c++/jni_common.h b/public/VectorPairHMM/src/main/c++/jni_common.h index 1cffea1cc..23c323246 100644 --- a/public/VectorPairHMM/src/main/c++/jni_common.h +++ b/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 diff --git a/public/VectorPairHMM/src/main/c++/jnidebug.h b/public/VectorPairHMM/src/main/c++/jnidebug.h index 7002b3637..7fcab2a51 100644 --- a/public/VectorPairHMM/src/main/c++/jnidebug.h +++ b/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 diff --git a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc b/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc index 98ebcde92..8a3f8b5bc 100644 --- a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc +++ b/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" diff --git a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h b/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h index 9e099dae0..18c2b0394 100644 --- a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h +++ b/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 /* Header for class org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM */ diff --git a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc b/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc index c28c24df1..0b54c8a81 100644 --- a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc +++ b/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" diff --git a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h b/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h index 3b07665f6..d820b4b26 100644 --- a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h +++ b/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 /* Header for class org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM */ diff --git a/public/VectorPairHMM/src/main/c++/pairhmm-1-base.cc b/public/VectorPairHMM/src/main/c++/pairhmm-1-base.cc index 78dbe296d..7ff219b88 100644 --- a/public/VectorPairHMM/src/main/c++/pairhmm-1-base.cc +++ b/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 diff --git a/public/VectorPairHMM/src/main/c++/pairhmm-template-kernel.cc b/public/VectorPairHMM/src/main/c++/pairhmm-template-kernel.cc index 77394f457..8c62b3c09 100644 --- a/public/VectorPairHMM/src/main/c++/pairhmm-template-kernel.cc +++ b/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 diff --git a/public/VectorPairHMM/src/main/c++/pairhmm-template-main.cc b/public/VectorPairHMM/src/main/c++/pairhmm-template-main.cc index cbcb8556d..5d9a05830 100644 --- a/public/VectorPairHMM/src/main/c++/pairhmm-template-main.cc +++ b/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" diff --git a/public/VectorPairHMM/src/main/c++/shift_template.c b/public/VectorPairHMM/src/main/c++/shift_template.c index 9750e1d8b..c591c6882 100644 --- a/public/VectorPairHMM/src/main/c++/shift_template.c +++ b/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 diff --git a/public/VectorPairHMM/src/main/c++/sse_function_instantiations.cc b/public/VectorPairHMM/src/main/c++/sse_function_instantiations.cc index f3fc110e0..550272494 100644 --- a/public/VectorPairHMM/src/main/c++/sse_function_instantiations.cc +++ b/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 diff --git a/public/VectorPairHMM/src/main/c++/template.h b/public/VectorPairHMM/src/main/c++/template.h index 3e52854a6..ce4dbfc86 100644 --- a/public/VectorPairHMM/src/main/c++/template.h +++ b/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_ diff --git a/public/VectorPairHMM/src/main/c++/utils.cc b/public/VectorPairHMM/src/main/c++/utils.cc index 35871948c..9f83cffa2 100644 --- a/public/VectorPairHMM/src/main/c++/utils.cc +++ b/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" diff --git a/public/VectorPairHMM/src/main/c++/utils.h b/public/VectorPairHMM/src/main/c++/utils.h index c1288d9e5..ce9ecd8c9 100644 --- a/public/VectorPairHMM/src/main/c++/utils.h +++ b/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 diff --git a/public/VectorPairHMM/src/main/c++/vector_defs.h b/public/VectorPairHMM/src/main/c++/vector_defs.h index 80b48ae99..2aca9565f 100644 --- a/public/VectorPairHMM/src/main/c++/vector_defs.h +++ b/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 diff --git a/public/VectorPairHMM/src/main/c++/vector_function_prototypes.h b/public/VectorPairHMM/src/main/c++/vector_function_prototypes.h index 67a2667e1..c0fddc394 100644 --- a/public/VectorPairHMM/src/main/c++/vector_function_prototypes.h +++ b/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]);