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|
Description: removing calls to doneNative methods, which are empty and cause
UnsatisfiedLinkError in the tests.
Author: Pierre Gruet <pgt@debian.org>
Forwarded: not-needed
Last-Update: 2025-08-31
--- a/src/main/java/com/intel/gkl/pairhmm/IntelPairHmm.java
+++ b/src/main/java/com/intel/gkl/pairhmm/IntelPairHmm.java
@@ -151,7 +151,6 @@
*/
@Override
public void done() {
- doneNative();
}
private native static void initNative(Class<?> readDataHolderClass,
@@ -162,6 +161,4 @@
private native void computeLikelihoodsNative(Object[] readDataArray,
Object[] haplotypeDataArray,
double[] likelihoodArray);
-
- private native void doneNative();
}
--- a/src/main/java/com/intel/gkl/pdhmm/IntelPDHMM.java
+++ b/src/main/java/com/intel/gkl/pdhmm/IntelPDHMM.java
@@ -122,7 +122,6 @@
@Override
public void done() {
- doneNative();
}
private static void checkArraySize(Object array, int expectedSize, String arrayName) {
@@ -214,7 +213,4 @@
private native void computeLikelihoodsNative(Object[] readDataArray,
Object[] haplotypeDataArray,
double[] likelihoodArray);
-
- private native static void doneNative();
-
}
--- a/src/main/java/com/intel/gkl/smithwaterman/IntelSmithWaterman.java
+++ b/src/main/java/com/intel/gkl/smithwaterman/IntelSmithWaterman.java
@@ -182,11 +182,9 @@
public void close()
{
- doneNative();
}
private native static void initNative();
private native static int alignNative(byte[] refArray, byte[] altArray, byte[] cigar, int match, int mismatch, int open, int extend, byte strategy);
- private native static void doneNative();
}
--- a/src/main/native/pairhmm/IntelPairHmm.cc
+++ b/src/main/native/pairhmm/IntelPairHmm.cc
@@ -179,14 +179,3 @@
DBG("Exit");
}
-
-
-/*
- * Class: com_intel_gkl_pairhmm_IntelPairHmm
- * Method: doneNative
- * Signature: ()V
- */
-JNIEXPORT void JNICALL Java_com_intel_gkl_pairhmm_IntelPairHmm_doneNative
-(JNIEnv* env, jobject obj)
-{
-}
--- a/src/main/native/pairhmm/IntelPairHmm.h
+++ b/src/main/native/pairhmm/IntelPairHmm.h
@@ -46,14 +46,6 @@
JNIEXPORT void JNICALL Java_com_intel_gkl_pairhmm_IntelPairHmm_computeLikelihoodsNative
(JNIEnv *, jobject, jobjectArray, jobjectArray, jdoubleArray);
-/*
- * Class: com_intel_gkl_pairhmm_IntelPairHmm
- * Method: doneNative
- * Signature: ()V
- */
-JNIEXPORT void JNICALL Java_com_intel_gkl_pairhmm_IntelPairHmm_doneNative
- (JNIEnv *, jobject);
-
#ifdef __cplusplus
}
#endif
--- a/src/main/native/pdhmm/IntelPDHMM.cc
+++ b/src/main/native/pdhmm/IntelPDHMM.cc
@@ -242,8 +242,3 @@
_mm_free(result);
return jresult;
}
-
-JNIEXPORT void JNICALL Java_com_intel_gkl_pdhmm_IntelPDHMM_doneNative(JNIEnv *env, jclass obj)
-{
- doneNative();
-}
--- a/src/main/native/pdhmm/IntelPDHMM.h
+++ b/src/main/native/pdhmm/IntelPDHMM.h
@@ -45,8 +45,6 @@
*/
JNIEXPORT void JNICALL Java_com_intel_gkl_pdhmm_IntelPDHMM_computeLikelihoodsNative(JNIEnv *, jobject, jobjectArray, jobjectArray, jdoubleArray);
- JNIEXPORT void JNICALL Java_com_intel_gkl_pdhmm_IntelPDHMM_doneNative(JNIEnv *env, jclass obj);
-
#ifdef __cplusplus
}
#endif
--- a/src/main/native/pdhmm/pdhmm-implementation.h
+++ b/src/main/native/pdhmm/pdhmm-implementation.h
@@ -324,11 +324,6 @@
return true;
}
-bool doneNative()
-{
- return true;
-}
-
int32_t computePDHMM(PDHMMInputData input)
{
ComputeConfig &config = ComputeConfig::getInstance();
--- a/src/main/native/smithwaterman/IntelSmithWaterman.cc
+++ b/src/main/native/smithwaterman/IntelSmithWaterman.cc
@@ -122,12 +122,3 @@
return offset;
}
-
-/*
- * Class: com_intel_gkl_smithwaterman_IntelSmithWaterman
- * Method: doneNative
- * Signature: ()V
- */
-JNIEXPORT void JNICALL Java_com_intel_gkl_smithwaterman_IntelSmithWaterman_doneNative(JNIEnv *, jclass)
-{
-}
--- a/src/main/native/smithwaterman/IntelSmithWaterman.h
+++ b/src/main/native/smithwaterman/IntelSmithWaterman.h
@@ -41,14 +41,6 @@
JNIEXPORT jint JNICALL Java_com_intel_gkl_smithwaterman_IntelSmithWaterman_alignNative
(JNIEnv *, jclass, jbyteArray, jbyteArray, jbyteArray, jint, jint, jint, jint, jbyte);
-/*
- * Class: com_intel_gkl_smithwaterman_IntelSmithWaterman
- * Method: doneNative
- * Signature: ()V
- */
-JNIEXPORT void JNICALL Java_com_intel_gkl_smithwaterman_IntelSmithWaterman_doneNative
- (JNIEnv *, jclass);
-
#ifdef __cplusplus
}
#endif
|
