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