Changed 'sting' to 'gatk' in the VectorLoglessPairHMM classes and the
C++ code
This commit is contained in:
Karthik Gururaj
Khalid Shakir
parent
3939971d78
commit
972a82d386
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@ -134,9 +134,9 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
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//Could not load from Java's library path - try unpacking from jar
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try
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{
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logger.debug("libVectorLoglessPairHMM not found in JVM library path - trying to unpack from StingUtils.jar");
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loadLibraryFromJar("/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so");
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logger.debug("libVectorLoglessPairHMM unpacked successfully from StingUtils.jar");
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logger.debug("libVectorLoglessPairHMM not found in JVM library path - trying to unpack from GATK jar file");
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loadLibraryFromJar("/org/broadinstitute/gatk/utils/pairhmm/libVectorLoglessPairHMM.so");
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logger.info("libVectorLoglessPairHMM unpacked successfully from GATK jar file");
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}
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catch(IOException ioe)
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{
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@ -74,14 +74,14 @@ DF=$(DEPDIR)/$(*).d
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#Common across libJNI and sandbox
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COMMON_SOURCES=utils.cc avx_function_instantiations.cc baseline.cc sse_function_instantiations.cc LoadTimeInitializer.cc
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#Part of libJNI
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LIBSOURCES=org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc Sandbox.cc $(COMMON_SOURCES)
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LIBSOURCES=org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.cc org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM.cc Sandbox.cc $(COMMON_SOURCES)
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SOURCES=$(LIBSOURCES) pairhmm-template-main.cc pairhmm-1-base.cc
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LIBOBJECTS=$(LIBSOURCES:.cc=.o)
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COMMON_OBJECTS=$(COMMON_SOURCES:.cc=.o)
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#No vectorization for these files
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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
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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
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#Use -xAVX for these files
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AVX_SOURCES=avx_function_instantiations.cc
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#Use -xSSE4.2 for these files
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@ -24,7 +24,7 @@
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#include "Sandbox.h"
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#include "org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h"
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#include "org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.h"
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#include "utils.h"
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#include "jni_common.h"
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/*
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@ -46,7 +46,7 @@ JNIEXPORT jlong JNICALL Java_Sandbox_jniGetMachineType
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JNIEXPORT void JNICALL Java_Sandbox_jniInitializeClassFieldsAndMachineMask
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(JNIEnv* env, jobject thisObject, jclass readDataHolderClass, jclass haplotypeDataHolderClass, jlong mask)
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{
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Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeClassFieldsAndMachineMask(env, thisObject, readDataHolderClass,
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Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeClassFieldsAndMachineMask(env, thisObject, readDataHolderClass,
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haplotypeDataHolderClass, mask);
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}
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@ -58,7 +58,7 @@ JNIEXPORT void JNICALL Java_Sandbox_jniInitializeClassFieldsAndMachineMask
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JNIEXPORT void JNICALL Java_Sandbox_jniInitializeHaplotypes
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(JNIEnv * env, jobject thisObject, jint numHaplotypes, jobjectArray haplotypeDataArray)
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{
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Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeHaplotypes(env, thisObject, numHaplotypes, haplotypeDataArray);
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Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeHaplotypes(env, thisObject, numHaplotypes, haplotypeDataArray);
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}
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/*
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@ -69,7 +69,7 @@ JNIEXPORT void JNICALL Java_Sandbox_jniInitializeHaplotypes
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JNIEXPORT void JNICALL Java_Sandbox_jniFinalizeRegion
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(JNIEnv * env, jobject thisObject)
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{
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Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniFinalizeRegion(env, thisObject);
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Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniFinalizeRegion(env, thisObject);
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}
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@ -82,7 +82,7 @@ JNIEXPORT void JNICALL Java_Sandbox_jniComputeLikelihoods
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(JNIEnv* env, jobject thisObject, jint numReads, jint numHaplotypes,
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jobjectArray readDataArray, jobjectArray haplotypeDataArray, jdoubleArray likelihoodArray, jint maxNumThreadsToUse)
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{
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Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods(env, thisObject,
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Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods(env, thisObject,
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numReads, numHaplotypes, readDataArray, haplotypeDataArray, likelihoodArray, maxNumThreadsToUse);
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}
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/*
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@ -92,7 +92,7 @@ JNIEXPORT void JNICALL Java_Sandbox_jniComputeLikelihoods
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*/
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JNIEXPORT void JNICALL Java_Sandbox_jniClose
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(JNIEnv* env, jobject thisObject)
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{ Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniClose(env, thisObject); }
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{ Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniClose(env, thisObject); }
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JNIEXPORT void JNICALL Java_Sandbox_doEverythingNative
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(JNIEnv* env, jobject thisObject, jstring fileNameString)
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@ -25,7 +25,7 @@
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#include "headers.h"
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#include "jni_common.h"
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#include "org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h"
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#include "org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM.h"
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#include "utils.h"
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#include "LoadTimeInitializer.h"
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#include "jnidebug.h"
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@ -33,7 +33,7 @@ DataHolder<double> g_double_dataholder;
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using namespace std;
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JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniInitialize
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JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniInitialize
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(JNIEnv* env, jobject thisObject,
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jint readMaxLength, jint haplotypeMaxLength)
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{
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@ -48,7 +48,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILogle
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++g_num_init_calls;
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}
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JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializeProbabilities
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JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializeProbabilities
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(JNIEnv* env, jclass thisObject,
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jobjectArray transition, jbyteArray insertionGOP, jbyteArray deletionGOP, jbyteArray overallGCP
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)
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@ -79,7 +79,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILogle
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}
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JNIEXPORT jdouble JNICALL
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Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializePriorsAndUpdateCells(
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Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializePriorsAndUpdateCells(
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JNIEnv* env, jobject thisObject,
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jboolean doInitialization, jint paddedReadLength, jint paddedHaplotypeLength,
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jbyteArray readBases, jbyteArray haplotypeBases, jbyteArray readQuals,
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@ -119,7 +119,7 @@ Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniInitialize
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}
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JNIEXPORT jdouble JNICALL
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Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniSubComputeReadLikelihoodGivenHaplotypeLog10(
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Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniSubComputeReadLikelihoodGivenHaplotypeLog10(
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JNIEnv* env, jobject thisObject,
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jint readLength, jint haplotypeLength,
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jbyteArray readBases, jbyteArray haplotypeBases, jbyteArray readQuals,
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@ -0,0 +1,86 @@
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/*Copyright (c) 2012 The Broad Institute
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*Permission is hereby granted, free of charge, to any person
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*obtaining a copy of this software and associated documentation
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*files (the "Software"), to deal in the Software without
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*restriction, including without limitation the rights to use,
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*copy, modify, merge, publish, distribute, sublicense, and/or sell
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*copies of the Software, and to permit persons to whom the
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*Software is furnished to do so, subject to the following
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*conditions:
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*The above copyright notice and this permission notice shall be
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*included in all copies or substantial portions of the Software.
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*THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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*EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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*OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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*NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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*HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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*WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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*FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR
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*THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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/* DO NOT EDIT THIS FILE - it is machine generated */
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#include <jni.h>
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/* Header for class org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM */
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#ifndef _Included_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM
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#define _Included_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM
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#ifdef __cplusplus
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extern "C" {
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#endif
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#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_TRISTATE_CORRECTION
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#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_TRISTATE_CORRECTION 3.0
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#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_dumpSandboxOnly
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#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_dumpSandboxOnly 0L
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#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug
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#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug 0L
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#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_verify
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#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_verify 1L
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#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug0_1
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#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug0_1 0L
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#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug1
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#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug1 0L
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#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug2
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#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug2 0L
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#undef org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug3
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#define org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_debug3 0L
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/*
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* Class: org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM
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* Method: jniInitialize
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* Signature: (II)V
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*/
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JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniInitialize
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(JNIEnv *, jobject, jint, jint);
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/*
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* Class: org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM
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* Method: jniInitializeProbabilities
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* Signature: ([[D[B[B[B)V
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*/
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JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializeProbabilities
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(JNIEnv *, jclass, jobjectArray, jbyteArray, jbyteArray, jbyteArray);
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/*
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* Class: org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM
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* Method: jniInitializePriorsAndUpdateCells
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* Signature: (ZII[B[B[BI)D
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*/
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JNIEXPORT jdouble JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializePriorsAndUpdateCells
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(JNIEnv *, jobject, jboolean, jint, jint, jbyteArray, jbyteArray, jbyteArray, jint);
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/*
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* Class: org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM
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* Method: jniSubComputeReadLikelihoodGivenHaplotypeLog10
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* Signature: (II[B[B[B[B[B[BI)D
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*/
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JNIEXPORT jdouble JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniSubComputeReadLikelihoodGivenHaplotypeLog10
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(JNIEnv *, jobject, jint, jint, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jbyteArray, jint);
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#ifdef __cplusplus
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}
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#endif
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#endif
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@ -25,14 +25,14 @@
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#include "headers.h"
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#include "jni_common.h"
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#include "org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h"
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#include "org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.h"
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//#include "template.h"
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#include "utils.h"
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#include "LoadTimeInitializer.h"
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using namespace std;
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JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniGetMachineType
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JNIEXPORT jlong JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniGetMachineType
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(JNIEnv* env, jobject thisObject)
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{
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return (jlong)get_machine_capabilities();
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@ -40,7 +40,7 @@ JNIEXPORT jlong JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLogles
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//Should be called only once for the whole Java process - initializes field ids for the classes JNIReadDataHolderClass
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//and JNIHaplotypeDataHolderClass
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JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeClassFieldsAndMachineMask
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JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeClassFieldsAndMachineMask
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(JNIEnv* env, jobject thisObject, jclass readDataHolderClass, jclass haplotypeDataHolderClass, jlong mask)
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{
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assert(readDataHolderClass);
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@ -138,7 +138,7 @@ vector<unsigned> g_haplotypeBasesLengths;
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//Since the list of haplotypes against which the reads are evaluated in PairHMM is the same for a region,
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//transfer the list only once
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//Works only for ST case as the haplotype data is stored in global variables
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JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeHaplotypes
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JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeHaplotypes
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(JNIEnv * env, jobject thisObject, jint numHaplotypes, jobjectArray haplotypeDataArray)
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{
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#ifdef SINGLE_THREADED_ONLY
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@ -150,7 +150,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLogless
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//Create a vector of testcases for computation - copy the references to bytearrays read/readQuals etc into the appropriate
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//testcase struct
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inline JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeTestcasesVector
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inline JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeTestcasesVector
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(JNIEnv* env, jint numReads, jint numHaplotypes, jobjectArray& readDataArray,
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vector<vector<pair<jbyteArray,jbyte*> > >& readBasesArrayVector,
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vector<pair<jbyteArray, jbyte*> >& haplotypeBasesArrayVector, vector<unsigned>& haplotypeBasesLengths,
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@ -271,7 +271,7 @@ inline void compute_testcases(vector<testcase>& tc_array, unsigned numTestCases,
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}
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//Inform the Java VM that we no longer need access to the read arrays (and free memory)
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inline JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniReleaseReadArrays
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inline JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniReleaseReadArrays
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(JNIEnv* env, vector<vector<pair<jbyteArray,jbyte*> > >& readBasesArrayVector)
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{
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//Release read arrays first
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@ -293,7 +293,7 @@ uint64_t g_sum = 0;
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//haplotypeDataArray - array of JNIHaplotypeDataHolderClass objects which contain the haplotypeBases
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//likelihoodArray - array of doubles to return results back to Java. Memory allocated by Java prior to JNI call
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//maxNumThreadsToUse - Max number of threads that OpenMP can use for the HMM computation
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JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods
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JNIEXPORT void JNICALL Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods
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(JNIEnv* env, jobject thisObject, jint numReads, jint numHaplotypes,
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jobjectArray readDataArray, jobjectArray haplotypeDataArray, jdoubleArray likelihoodArray, jint maxNumThreadsToUse)
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{
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@ -329,7 +329,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLogless
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initializeHaplotypes(env, thisObject, numHaplotypes, haplotypeDataArray, haplotypeBasesArrayVector, haplotypeBasesLengths);
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#endif
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//Copy byte array references from Java memory into vector of testcase structs
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Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniInitializeTestcasesVector(env,
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Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniInitializeTestcasesVector(env,
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numReads, numHaplotypes, readDataArray, readBasesArrayVector, haplotypeBasesArrayVector, haplotypeBasesLengths, tc_array);
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#ifdef DO_PROFILING
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@ -375,7 +375,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLogless
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get_time(&start_time);
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#endif
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RELEASE_DOUBLE_ARRAY_ELEMENTS(likelihoodArray, likelihoodDoubleArray, 0); //release mode 0, copy back results to Java memory (if copy made)
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Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniReleaseReadArrays(env, readBasesArrayVector);
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Java_org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM_jniReleaseReadArrays(env, readBasesArrayVector);
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#ifndef SINGLE_THREADED_ONLY
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releaseHaplotypes(env, thisObject, haplotypeBasesArrayVector, haplotypeBasesLengths);
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#endif
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|
|
@ -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
|
||||
|
|
@ -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 <jni.h>
|
||||
/* 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
|
||||
|
|
@ -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 <jni.h>
|
||||
/* 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
|
||||
|
|
@ -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 <jni.h>
|
||||
/* 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
|
||||
Binary file not shown.
Loading…
Reference in New Issue