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Changed 'sting' to 'gatk' in the VectorLoglessPairHMM classes and the 

C++ code
This commit is contained in:
Karthik Gururaj 2014-05-09 10:43:01 -07:00 committed by Khalid Shakir
parent 3939971d78
commit 972a82d386
10 changed files with 209 additions and 227 deletions
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6
protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/utils/pairhmm/VectorLoglessPairHMM.java
View File

@ -134,9 +134,9 @@ public class VectorLoglessPairHMM extends JNILoglessPairHMM {
//Could not load from Java's library path - try unpacking from jar //Could not load from Java's library path - try unpacking from jar
try try
{ {
logger.debug("libVectorLoglessPairHMM not found in JVM library path - trying to unpack from StingUtils.jar"); logger.debug("libVectorLoglessPairHMM not found in JVM library path - trying to unpack from GATK jar file");
loadLibraryFromJar("/org/broadinstitute/sting/utils/pairhmm/libVectorLoglessPairHMM.so"); loadLibraryFromJar("/org/broadinstitute/gatk/utils/pairhmm/libVectorLoglessPairHMM.so");
logger.debug("libVectorLoglessPairHMM unpacked successfully from StingUtils.jar"); logger.info("libVectorLoglessPairHMM unpacked successfully from GATK jar file");
} }
catch(IOException ioe) catch(IOException ioe)
{ {

4
public/VectorPairHMM/src/main/c++/Makefile
View File

@ -74,14 +74,14 @@ DF=$(DEPDIR)/$(*).d
#Common across libJNI and sandbox #Common across libJNI and sandbox
COMMON_SOURCES=utils.cc avx_function_instantiations.cc baseline.cc sse_function_instantiations.cc LoadTimeInitializer.cc COMMON_SOURCES=utils.cc avx_function_instantiations.cc baseline.cc sse_function_instantiations.cc LoadTimeInitializer.cc
#Part of libJNI #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 SOURCES=$(LIBSOURCES) pairhmm-template-main.cc pairhmm-1-base.cc
LIBOBJECTS=$(LIBSOURCES:.cc=.o) LIBOBJECTS=$(LIBSOURCES:.cc=.o)
COMMON_OBJECTS=$(COMMON_SOURCES:.cc=.o) COMMON_OBJECTS=$(COMMON_SOURCES:.cc=.o)
#No vectorization for these files #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 #Use -xAVX for these files
AVX_SOURCES=avx_function_instantiations.cc AVX_SOURCES=avx_function_instantiations.cc
#Use -xSSE4.2 for these files #Use -xSSE4.2 for these files

12
public/VectorPairHMM/src/main/c++/Sandbox.cc
View File

@ -24,7 +24,7 @@
#include "Sandbox.h" #include "Sandbox.h"
#include "org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h" #include "org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.h"
#include "utils.h" #include "utils.h"
#include "jni_common.h" #include "jni_common.h"
/* /*
@ -46,7 +46,7 @@ JNIEXPORT jlong JNICALL Java_Sandbox_jniGetMachineType
JNIEXPORT void JNICALL Java_Sandbox_jniInitializeClassFieldsAndMachineMask JNIEXPORT void JNICALL Java_Sandbox_jniInitializeClassFieldsAndMachineMask
(JNIEnv* env, jobject thisObject, jclass readDataHolderClass, jclass haplotypeDataHolderClass, jlong mask) (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); haplotypeDataHolderClass, mask);
} }
@ -58,7 +58,7 @@ JNIEXPORT void JNICALL Java_Sandbox_jniInitializeClassFieldsAndMachineMask
JNIEXPORT void JNICALL Java_Sandbox_jniInitializeHaplotypes JNIEXPORT void JNICALL Java_Sandbox_jniInitializeHaplotypes
(JNIEnv * env, jobject thisObject, jint numHaplotypes, jobjectArray haplotypeDataArray) (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 JNIEXPORT void JNICALL Java_Sandbox_jniFinalizeRegion
(JNIEnv * env, jobject thisObject) (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, (JNIEnv* env, jobject thisObject, jint numReads, jint numHaplotypes,
jobjectArray readDataArray, jobjectArray haplotypeDataArray, jdoubleArray likelihoodArray, jint maxNumThreadsToUse) 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); numReads, numHaplotypes, readDataArray, haplotypeDataArray, likelihoodArray, maxNumThreadsToUse);
} }
/* /*
@ -92,7 +92,7 @@ JNIEXPORT void JNICALL Java_Sandbox_jniComputeLikelihoods
*/ */
JNIEXPORT void JNICALL Java_Sandbox_jniClose JNIEXPORT void JNICALL Java_Sandbox_jniClose
(JNIEnv* env, jobject thisObject) (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 JNIEXPORT void JNICALL Java_Sandbox_doEverythingNative
(JNIEnv* env, jobject thisObject, jstring fileNameString) (JNIEnv* env, jobject thisObject, jstring fileNameString)

10
public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.cc → public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM.cc
View File

@ -25,7 +25,7 @@
#include "headers.h" #include "headers.h"
#include "jni_common.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 "utils.h"
#include "LoadTimeInitializer.h" #include "LoadTimeInitializer.h"
#include "jnidebug.h" #include "jnidebug.h"
@ -33,7 +33,7 @@ DataHolder<double> g_double_dataholder;
using namespace std; 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, (JNIEnv* env, jobject thisObject,
jint readMaxLength, jint haplotypeMaxLength) jint readMaxLength, jint haplotypeMaxLength)
{ {
@ -48,7 +48,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILogle
++g_num_init_calls; ++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, (JNIEnv* env, jclass thisObject,
jobjectArray transition, jbyteArray insertionGOP, jbyteArray deletionGOP, jbyteArray overallGCP 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 JNIEXPORT jdouble JNICALL
Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializePriorsAndUpdateCells( Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniInitializePriorsAndUpdateCells(
JNIEnv* env, jobject thisObject, JNIEnv* env, jobject thisObject,
jboolean doInitialization, jint paddedReadLength, jint paddedHaplotypeLength, jboolean doInitialization, jint paddedReadLength, jint paddedHaplotypeLength,
jbyteArray readBases, jbyteArray haplotypeBases, jbyteArray readQuals, jbyteArray readBases, jbyteArray haplotypeBases, jbyteArray readQuals,
@ -119,7 +119,7 @@ Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniInitialize
} }
JNIEXPORT jdouble JNICALL JNIEXPORT jdouble JNICALL
Java_org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM_jniSubComputeReadLikelihoodGivenHaplotypeLog10( Java_org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM_jniSubComputeReadLikelihoodGivenHaplotypeLog10(
JNIEnv* env, jobject thisObject, JNIEnv* env, jobject thisObject,
jint readLength, jint haplotypeLength, jint readLength, jint haplotypeLength,
jbyteArray readBases, jbyteArray haplotypeBases, jbyteArray readQuals, jbyteArray readBases, jbyteArray haplotypeBases, jbyteArray readQuals,

86
public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_DebugJNILoglessPairHMM.h 100644
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@ -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 <jni.h>
/* 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

22
public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.cc → public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.cc
View File

@ -25,14 +25,14 @@
#include "headers.h" #include "headers.h"
#include "jni_common.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 "template.h"
#include "utils.h" #include "utils.h"
#include "LoadTimeInitializer.h" #include "LoadTimeInitializer.h"
using namespace std; 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) (JNIEnv* env, jobject thisObject)
{ {
return (jlong)get_machine_capabilities(); 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 //Should be called only once for the whole Java process - initializes field ids for the classes JNIReadDataHolderClass
//and JNIHaplotypeDataHolderClass //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) (JNIEnv* env, jobject thisObject, jclass readDataHolderClass, jclass haplotypeDataHolderClass, jlong mask)
{ {
assert(readDataHolderClass); assert(readDataHolderClass);
@ -138,7 +138,7 @@ vector<unsigned> g_haplotypeBasesLengths;
//Since the list of haplotypes against which the reads are evaluated in PairHMM is the same for a region, //Since the list of haplotypes against which the reads are evaluated in PairHMM is the same for a region,
//transfer the list only once //transfer the list only once
//Works only for ST case as the haplotype data is stored in global variables //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) (JNIEnv * env, jobject thisObject, jint numHaplotypes, jobjectArray haplotypeDataArray)
{ {
#ifdef SINGLE_THREADED_ONLY #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 //Create a vector of testcases for computation - copy the references to bytearrays read/readQuals etc into the appropriate
//testcase struct //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, (JNIEnv* env, jint numReads, jint numHaplotypes, jobjectArray& readDataArray,
vector<vector<pair<jbyteArray,jbyte*> > >& readBasesArrayVector, vector<vector<pair<jbyteArray,jbyte*> > >& readBasesArrayVector,
vector<pair<jbyteArray, jbyte*> >& haplotypeBasesArrayVector, vector<unsigned>& haplotypeBasesLengths, vector<pair<jbyteArray, jbyte*> >& haplotypeBasesArrayVector, vector<unsigned>& haplotypeBasesLengths,
@ -271,7 +271,7 @@ inline void compute_testcases(vector<testcase>& tc_array, unsigned numTestCases,
} }
//Inform the Java VM that we no longer need access to the read arrays (and free memory) //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<vector<pair<jbyteArray,jbyte*> > >& readBasesArrayVector) (JNIEnv* env, vector<vector<pair<jbyteArray,jbyte*> > >& readBasesArrayVector)
{ {
//Release read arrays first //Release read arrays first
@ -293,7 +293,7 @@ uint64_t g_sum = 0;
//haplotypeDataArray - array of JNIHaplotypeDataHolderClass objects which contain the haplotypeBases //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 //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 //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, (JNIEnv* env, jobject thisObject, jint numReads, jint numHaplotypes,
jobjectArray readDataArray, jobjectArray haplotypeDataArray, jdoubleArray likelihoodArray, jint maxNumThreadsToUse) 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); initializeHaplotypes(env, thisObject, numHaplotypes, haplotypeDataArray, haplotypeBasesArrayVector, haplotypeBasesLengths);
#endif #endif
//Copy byte array references from Java memory into vector of testcase structs //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); numReads, numHaplotypes, readDataArray, readBasesArrayVector, haplotypeBasesArrayVector, haplotypeBasesLengths, tc_array);
#ifdef DO_PROFILING #ifdef DO_PROFILING
@ -375,7 +375,7 @@ JNIEXPORT void JNICALL Java_org_broadinstitute_sting_utils_pairhmm_VectorLogless
get_time(&start_time); get_time(&start_time);
#endif #endif
RELEASE_DOUBLE_ARRAY_ELEMENTS(likelihoodArray, likelihoodDoubleArray, 0); //release mode 0, copy back results to Java memory (if copy made) 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 #ifndef SINGLE_THREADED_ONLY
releaseHaplotypes(env, thisObject, haplotypeBasesArrayVector, haplotypeBasesLengths); releaseHaplotypes(env, thisObject, haplotypeBasesArrayVector, haplotypeBasesLengths);
#endif #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 //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) (JNIEnv * env, jobject thisObject)
{ {
#ifdef SINGLE_THREADED_ONLY #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) (JNIEnv* env, jobject thisObject)
{ {
#ifdef DO_PROFILING #ifdef DO_PROFILING

96
public/VectorPairHMM/src/main/c++/org_broadinstitute_gatk_utils_pairhmm_VectorLoglessPairHMM.h 100644
View File

@ -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

96
public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_DebugJNILoglessPairHMM.h
View File

@ -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

104
public/VectorPairHMM/src/main/c++/org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM.h
View File

@ -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

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public/gatk-utils/src/main/resources/org/broadinstitute/gatk/utils/pairhmm/libVectorLoglessPairHMM.so
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