diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java index df78c89f6..233c1de17 100644 --- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java +++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java @@ -134,9 +134,9 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM { //Could not load from Java's library path - try unpacking from jar try { - logger.debug("libVectorLoglessPairHMM not found in JVM library path - trying to unpack from StingUtils.jar"); - loadLibraryFromJar("/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so"); - logger.debug("libVectorLoglessPairHMM unpacked successfully from StingUtils.jar"); + logger.debug("libVectorLoglessPairHMM not found in JVM library path - trying to unpack from GATK jar file"); + loadLibraryFromJar("/org/broadinstitute/gatk/utils/pairhmm/libVectorLoglessPairHMM.so"); + logger.info("libVectorLoglessPairHMM unpacked successfully from GATK jar file"); } catch(IOException ioe) { diff --git a/public/VectorPairHMM/src/main/c++/Makefile b/public/VectorPairHMM/src/main/c++/Makefile index 57fcc4e6d..0fae1e815 100644 --- a/public/VectorPairHMM/src/main/c++/Makefile +++ b/public/VectorPairHMM/src/main/c++/Makefile @@ -74,14 +74,14 @@ DF=$(DEPDIR)/$(*).d #Common across libJNI and sandbox COMMON_SOURCES=utils.cc avx_function_instantiations.cc baseline.cc sse_function_instantiations.cc LoadTimeInitializer.cc #Part of libJNI -LIBSOURCES=org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc Sandbox.cc $(COMMON_SOURCES) +LIBSOURCES=org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.cc org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM.cc Sandbox.cc $(COMMON_SOURCES) SOURCES=$(LIBSOURCES) pairhmm-template-main.cc pairhmm-1-base.cc LIBOBJECTS=$(LIBSOURCES:.cc=.o) COMMON_OBJECTS=$(COMMON_SOURCES:.cc=.o) #No vectorization for these files -NO_VECTOR_SOURCES=org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc pairhmm-template-main.cc pairhmm-1-base.cc utils.cc baseline.cc LoadTimeInitializer.cc Sandbox.cc +NO_VECTOR_SOURCES=org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.cc org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM.cc pairhmm-template-main.cc pairhmm-1-base.cc utils.cc baseline.cc LoadTimeInitializer.cc Sandbox.cc #Use -xAVX for these files AVX_SOURCES=avx_function_instantiations.cc #Use -xSSE4.2 for these files diff --git a/public/VectorPairHMM/src/main/c++/Sandbox.cc b/public/VectorPairHMM/src/main/c++/Sandbox.cc index 985b19ae9..a4c2b73ec 100644 --- a/public/VectorPairHMM/src/main/c++/Sandbox.cc +++ b/public/VectorPairHMM/src/main/c++/Sandbox.cc @@ -24,7 +24,7 @@ #include "Sandbox.h" -#include "org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h" +#include "org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.h" #include "utils.h" #include "jni_common.h" /* @@ -46,7 +46,7 @@ JNIEXPORT jlong JNICALL Java_Sandbox_jniGetMachineType JNIEXPORT void JNICALL Java_Sandbox_jniInitializeClassFieldsAndMachineMask (JNIEnv* env, jobject thisObject, jclass readDataHolderClass, jclass haplotypeDataHolderClass, jlong mask) { - Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeClassFieldsAndMachineMask(env, thisObject, readDataHolderClass, + Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeClassFieldsAndMachineMask(env, thisObject, readDataHolderClass, haplotypeDataHolderClass, mask); } @@ -58,7 +58,7 @@ JNIEXPORT void JNICALL Java_Sandbox_jniInitializeClassFieldsAndMachineMask JNIEXPORT void JNICALL Java_Sandbox_jniInitializeHaplotypes (JNIEnv * env, jobject thisObject, jint numHaplotypes, jobjectArray haplotypeDataArray) { - Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeHaplotypes(env, thisObject, numHaplotypes, haplotypeDataArray); + Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeHaplotypes(env, thisObject, numHaplotypes, haplotypeDataArray); } /* @@ -69,7 +69,7 @@ JNIEXPORT void JNICALL Java_Sandbox_jniInitializeHaplotypes JNIEXPORT void JNICALL Java_Sandbox_jniFinalizeRegion (JNIEnv * env, jobject thisObject) { - Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniFinalizeRegion(env, thisObject); + Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniFinalizeRegion(env, thisObject); } @@ -82,7 +82,7 @@ JNIEXPORT void JNICALL Java_Sandbox_jniComputeLikelihoods (JNIEnv* env, jobject thisObject, jint numReads, jint numHaplotypes, jobjectArray readDataArray, jobjectArray haplotypeDataArray, jdoubleArray likelihoodArray, jint maxNumThreadsToUse) { - Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods(env, thisObject, + Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods(env, thisObject, numReads, numHaplotypes, readDataArray, haplotypeDataArray, likelihoodArray, maxNumThreadsToUse); } /* @@ -92,7 +92,7 @@ JNIEXPORT void JNICALL Java_Sandbox_jniComputeLikelihoods */ JNIEXPORT void JNICALL Java_Sandbox_jniClose (JNIEnv* env, jobject thisObject) -{ Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniClose(env, thisObject); } +{ Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniClose(env, thisObject); } JNIEXPORT void JNICALL Java_Sandbox_doEverythingNative (JNIEnv* env, jobject thisObject, jstring fileNameString) diff --git a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc b/public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM.cc similarity index 93% rename from public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc rename to public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM.cc index 641e2016d..42a9237c5 100644 --- a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc +++ b/public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM.cc @@ -25,7 +25,7 @@ #include "headers.h" #include "jni_common.h" -#include "org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h" +#include "org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM.h" #include "utils.h" #include "LoadTimeInitializer.h" #include "jnidebug.h" @@ -33,7 +33,7 @@ DataHolder g_double_dataholder; using namespace std; -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniInitialize +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniInitialize (JNIEnv* env, jobject thisObject, jint readMaxLength, jint haplotypeMaxLength) { @@ -48,7 +48,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILogle ++g_num_init_calls; } -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializeProbabilities +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializeProbabilities (JNIEnv* env, jclass thisObject, jobjectArray transition, jbyteArray insertionGOP, jbyteArray deletionGOP, jbyteArray overallGCP ) @@ -79,7 +79,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILogle } JNIEXPORT jdouble JNICALL -Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializePriorsAndUpdateCells( +Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializePriorsAndUpdateCells( JNIEnv* env, jobject thisObject, jboolean doInitialization, jint paddedReadLength, jint paddedHaplotypeLength, jbyteArray readBases, jbyteArray haplotypeBases, jbyteArray readQuals, @@ -119,7 +119,7 @@ Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniInitialize } JNIEXPORT jdouble JNICALL -Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniSubComputeReadLikelihoodGivenHaplotypeLog10( +Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniSubComputeReadLikelihoodGivenHaplotypeLog10( JNIEnv* env, jobject thisObject, jint readLength, jint haplotypeLength, jbyteArray readBases, jbyteArray haplotypeBases, jbyteArray readQuals, diff --git a/public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM.h b/public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM.h new file mode 100644 index 000000000..6fb440c5a --- /dev/null +++ b/public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM.h @@ -0,0 +1,86 @@ +/*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_gatk_utils_pairhmm_DebugJNILoglessPairHMM */ + +#ifndef _Included_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM +#define _Included_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM +#ifdef __cplusplus +extern "C" { +#endif +#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_TRISTATE_CORRECTION +#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_TRISTATE_CORRECTION 3.0 +#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_dumpSandboxOnly +#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_dumpSandboxOnly 0L +#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug +#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug 0L +#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_verify +#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_verify 1L +#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug0_1 +#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug0_1 0L +#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug1 +#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug1 0L +#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug2 +#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug2 0L +#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug3 +#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug3 0L +/* + * Class: org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM + * Method: jniInitialize + * Signature: (II)V + */ +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniInitialize + (JNIEnv *, jobject, jint, jint); + +/* + * Class: org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM + * Method: jniInitializeProbabilities + * Signature: ([[D[B[B[B)V + */ +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializeProbabilities + (JNIEnv *, jclass, jobjectArray, jbyteArray, jbyteArray, jbyteArray); + +/* + * Class: org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM + * Method: jniInitializePriorsAndUpdateCells + * Signature: (ZII[B[B[BI)D + */ +JNIEXPORT jdouble JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializePriorsAndUpdateCells + (JNIEnv *, jobject, jboolean, jint, jint, jbyteArray, jbyteArray, jbyteArray, jint); + +/* + * Class: org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM + * Method: jniSubComputeReadLikelihoodGivenHaplotypeLog10 + * Signature: (II[B[B[B[B[B[BI)D + */ +JNIEXPORT jdouble JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniSubComputeReadLikelihoodGivenHaplotypeLog10 + (JNIEnv *, jobject, jint, jint, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jint); + +#ifdef __cplusplus +} +#endif +#endif diff --git a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc b/public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.cc similarity index 93% rename from public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc rename to public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.cc index 9c00c45af..d9d268462 100644 --- a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc +++ b/public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.cc @@ -25,14 +25,14 @@ #include "headers.h" #include "jni_common.h" -#include "org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h" +#include "org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.h" //#include "template.h" #include "utils.h" #include "LoadTimeInitializer.h" using namespace std; -JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniGetMachineType +JNIEXPORT jlong JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniGetMachineType (JNIEnv* env, jobject thisObject) { return (jlong)get_machine_capabilities(); @@ -40,7 +40,7 @@ JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLogles //Should be called only once for the whole Java process - initializes field ids for the classes JNIReadDataHolderClass //and JNIHaplotypeDataHolderClass -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeClassFieldsAndMachineMask +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeClassFieldsAndMachineMask (JNIEnv* env, jobject thisObject, jclass readDataHolderClass, jclass haplotypeDataHolderClass, jlong mask) { assert(readDataHolderClass); @@ -138,7 +138,7 @@ vector g_haplotypeBasesLengths; //Since the list of haplotypes against which the reads are evaluated in PairHMM is the same for a region, //transfer the list only once //Works only for ST case as the haplotype data is stored in global variables -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeHaplotypes +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeHaplotypes (JNIEnv * env, jobject thisObject, jint numHaplotypes, jobjectArray haplotypeDataArray) { #ifdef SINGLE_THREADED_ONLY @@ -150,7 +150,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLogless //Create a vector of testcases for computation - copy the references to bytearrays read/readQuals etc into the appropriate //testcase struct -inline JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeTestcasesVector +inline JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeTestcasesVector (JNIEnv* env, jint numReads, jint numHaplotypes, jobjectArray& readDataArray, vector > >& readBasesArrayVector, vector >& haplotypeBasesArrayVector, vector& haplotypeBasesLengths, @@ -271,7 +271,7 @@ inline void compute_testcases(vector& tc_array, unsigned numTestCases, } //Inform the Java VM that we no longer need access to the read arrays (and free memory) -inline JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniReleaseReadArrays +inline JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniReleaseReadArrays (JNIEnv* env, vector > >& readBasesArrayVector) { //Release read arrays first @@ -293,7 +293,7 @@ uint64_t g_sum = 0; //haplotypeDataArray - array of JNIHaplotypeDataHolderClass objects which contain the haplotypeBases //likelihoodArray - array of doubles to return results back to Java. Memory allocated by Java prior to JNI call //maxNumThreadsToUse - Max number of threads that OpenMP can use for the HMM computation -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods (JNIEnv* env, jobject thisObject, jint numReads, jint numHaplotypes, jobjectArray readDataArray, jobjectArray haplotypeDataArray, jdoubleArray likelihoodArray, jint maxNumThreadsToUse) { @@ -329,7 +329,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLogless initializeHaplotypes(env, thisObject, numHaplotypes, haplotypeDataArray, haplotypeBasesArrayVector, haplotypeBasesLengths); #endif //Copy byte array references from Java memory into vector of testcase structs - Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeTestcasesVector(env, + Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeTestcasesVector(env, numReads, numHaplotypes, readDataArray, readBasesArrayVector, haplotypeBasesArrayVector, haplotypeBasesLengths, tc_array); #ifdef DO_PROFILING @@ -375,7 +375,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLogless get_time(&start_time); #endif RELEASE_DOUBLE_ARRAY_ELEMENTS(likelihoodArray, likelihoodDoubleArray, 0); //release mode 0, copy back results to Java memory (if copy made) - Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniReleaseReadArrays(env, readBasesArrayVector); + Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniReleaseReadArrays(env, readBasesArrayVector); #ifndef SINGLE_THREADED_ONLY releaseHaplotypes(env, thisObject, haplotypeBasesArrayVector, haplotypeBasesLengths); #endif @@ -394,7 +394,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLogless } //If single threaded, release haplotypes at the end of a region -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniFinalizeRegion +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniFinalizeRegion (JNIEnv * env, jobject thisObject) { #ifdef SINGLE_THREADED_ONLY @@ -403,7 +403,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLogless } -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniClose +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniClose (JNIEnv* env, jobject thisObject) { #ifdef DO_PROFILING diff --git a/public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.h b/public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.h new file mode 100644 index 000000000..6172da5c8 --- /dev/null +++ b/public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.h @@ -0,0 +1,96 @@ +/*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_gatk_utils_pairhmm_VectorLoglessPairHMM */ + +#ifndef _Included_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM +#define _Included_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM +#ifdef __cplusplus +extern "C" { +#endif +#undef org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_TRISTATE_CORRECTION +#define org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_TRISTATE_CORRECTION 3.0 +#undef org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_sse41Mask +#define org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_sse41Mask 1LL +#undef org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_sse42Mask +#define org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_sse42Mask 2LL +#undef org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_avxMask +#define org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_avxMask 4LL +#undef org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_enableAll +#define org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_enableAll -1LL +/* + * Class: org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM + * Method: jniGetMachineType + * Signature: ()J + */ +JNIEXPORT jlong JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniGetMachineType + (JNIEnv *, jobject); + +/* + * Class: org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM + * Method: jniInitializeClassFieldsAndMachineMask + * Signature: (Ljava/lang/Class;Ljava/lang/Class;J)V + */ +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeClassFieldsAndMachineMask + (JNIEnv *, jobject, jclass, jclass, jlong); + +/* + * Class: org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM + * Method: jniInitializeHaplotypes + * Signature: (I[Lorg/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM/JNIHaplotypeDataHolderClass;)V + */ +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeHaplotypes + (JNIEnv *, jobject, jint, jobjectArray); + +/* + * Class: org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM + * Method: jniFinalizeRegion + * Signature: ()V + */ +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniFinalizeRegion + (JNIEnv *, jobject); + +/* + * Class: org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM + * Method: jniComputeLikelihoods + * Signature: (II[Lorg/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM/JNIReadDataHolderClass;[Lorg/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM/JNIHaplotypeDataHolderClass;[DI)V + */ +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods + (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jdoubleArray, jint); + +/* + * Class: org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM + * Method: jniClose + * Signature: ()V + */ +JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniClose + (JNIEnv *, jobject); + +#ifdef __cplusplus +} +#endif +#endif 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 deleted file mode 100644 index 18c2b0394..000000000 --- a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h +++ /dev/null @@ -1,96 +0,0 @@ -/*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 */ - -#ifndef _Included_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM -#define _Included_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM -#ifdef __cplusplus -extern "C" { -#endif -#undef org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_TRISTATE_CORRECTION -#define org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_TRISTATE_CORRECTION 3.0 -#undef org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_matchToMatch -#define org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_matchToMatch 0L -#undef org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_indelToMatch -#define org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_indelToMatch 1L -#undef org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_matchToInsertion -#define org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_matchToInsertion 2L -#undef org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_insertionToInsertion -#define org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_insertionToInsertion 3L -#undef org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_matchToDeletion -#define org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_matchToDeletion 4L -#undef org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_deletionToDeletion -#define org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_deletionToDeletion 5L -#undef org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_debug -#define org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_debug 0L -#undef org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_verify -#define org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_verify 0L -#undef org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_debug0_1 -#define org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_debug0_1 0L -#undef org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_debug1 -#define org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_debug1 0L -#undef org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_debug2 -#define org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_debug2 0L -#undef org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_debug3 -#define org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_debug3 0L -/* - * Class: org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM - * Method: jniInitialize - * Signature: (II)V - */ -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniInitialize - (JNIEnv *, jobject, jint, jint); - -/* - * Class: org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM - * Method: jniInitializeProbabilities - * Signature: ([[D[B[B[B)V - */ -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializeProbabilities - (JNIEnv *, jclass, jobjectArray, jbyteArray, jbyteArray, jbyteArray); - -/* - * Class: org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM - * Method: jniInitializePriorsAndUpdateCells - * Signature: (ZII[B[B[BI)D - */ -JNIEXPORT jdouble JNICALL Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializePriorsAndUpdateCells - (JNIEnv *, jobject, jboolean, jint, jint, jbyteArray, jbyteArray, jbyteArray, jint); - -/* - * Class: org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM - * Method: jniSubComputeReadLikelihoodGivenHaplotypeLog10 - * Signature: (II[B[B[B[B[B[BI)D - */ -JNIEXPORT jdouble JNICALL Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniSubComputeReadLikelihoodGivenHaplotypeLog10 - (JNIEnv *, jobject, jint, jint, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jint); - -#ifdef __cplusplus -} -#endif -#endif 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 deleted file mode 100644 index d820b4b26..000000000 --- a/public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h +++ /dev/null @@ -1,104 +0,0 @@ -/*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 */ - -#ifndef _Included_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM -#define _Included_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM -#ifdef __cplusplus -extern "C" { -#endif -#undef org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_TRISTATE_CORRECTION -#define org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_TRISTATE_CORRECTION 3.0 -#undef org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_matchToMatch -#define org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_matchToMatch 0L -#undef org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_indelToMatch -#define org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_indelToMatch 1L -#undef org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_matchToInsertion -#define org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_matchToInsertion 2L -#undef org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_insertionToInsertion -#define org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_insertionToInsertion 3L -#undef org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_matchToDeletion -#define org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_matchToDeletion 4L -#undef org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_deletionToDeletion -#define org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_deletionToDeletion 5L -#undef org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_sse42Mask -#define org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_sse42Mask 1LL -#undef org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_avxMask -#define org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_avxMask 2LL -/* - * Class: org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM - * Method: jniGetMachineType - * Signature: ()J - */ -JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniGetMachineType - (JNIEnv *, jobject); - -/* - * Class: org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM - * Method: jniClose - * Signature: ()V - */ -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniClose - (JNIEnv *, jobject); - -/* - * Class: org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM - * Method: jniInitializeClassFieldsAndMachineMask - * Signature: (Ljava/lang/Class;Ljava/lang/Class;J)V - */ -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeClassFieldsAndMachineMask - (JNIEnv *, jobject, jclass, jclass, jlong); - -/* - * Class: org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM - * Method: jniInitializeHaplotypes - * Signature: (I[Lorg/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM/JNIHaplotypeDataHolderClass;)V - */ -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeHaplotypes - (JNIEnv *, jobject, jint, jobjectArray); - -/* - * Class: org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM - * Method: jniFinalizeRegion - * Signature: ()V - */ -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniFinalizeRegion - (JNIEnv *, jobject); - -/* - * Class: org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM - * Method: jniComputeLikelihoods - * Signature: (II[Lorg/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM/JNIReadDataHolderClass;[Lorg/broadinstitute/sting/utils/pairhmm/VectorLoglessPairHMM/JNIHaplotypeDataHolderClass;[DI)V - */ -JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods - (JNIEnv *, jobject, jint, jint, jobjectArray, jobjectArray, jdoubleArray, jint); - -#ifdef __cplusplus -} -#endif -#endif diff --git a/public/gatk-utils/src/main/resources/org/broadinstitute/gatk/utils/pairhmm/libVectorLoglessPairHMM.so b/public/gatk-utils/src/main/resources/org/broadinstitute/gatk/utils/pairhmm/libVectorLoglessPairHMM.so index 2a55b7b0f..a27f4e6bc 100644 Binary files a/public/gatk-utils/src/main/resources/org/broadinstitute/gatk/utils/pairhmm/libVectorLoglessPairHMM.so and b/public/gatk-utils/src/main/resources/org/broadinstitute/gatk/utils/pairhmm/libVectorLoglessPairHMM.so differ