build.gradle | 110 17 + 93 - 0 !
1 file changed, 17 insertions(+), 93 deletions(-)

 adapt build to debian packaging needs

build.gradle | 7 4 + 3 - 0 !
1 file changed, 4 insertions(+), 3 deletions(-)

 the cmake build task should be run only once.
 Yet it would be called twice when we run the build and then the tests. We add
 a check to prevent such situation.

build.gradle | 1 1 + 0 - 0 !
src/main/java/com/intel/gkl/NativeLibraryLoader.java | 33 2 + 31 - 0 !
2 files changed, 3 insertions(+), 31 deletions(-)

 loading the native library from /usr/lib/jni as we don't want to
 bundle the shared libraries into the jar.

src/main/java/com/intel/gkl/pairhmm/IntelPairHmm.java | 2 1 + 1 - 0 !
src/main/java/com/intel/gkl/smithwaterman/IntelSmithWaterman.java | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 marking a method as final as it is called in the constructor, this
 is to avoid failing to build with OpenJDK-21:
 /<<PKGBUILDDIR>>/src/main/java/com/intel/gkl/smithwaterman/IntelSmithWaterman.java:64: warning: [this-escape] possible 'this' escape before subclass is fully initialized
        setNativeLibraryName(NATIVE_LIBRARY_NAME);
                            ^

src/main/java/com/intel/gkl/pairhmm/IntelPairHmm.java | 3 0 + 3 - 0 !
src/main/java/com/intel/gkl/pdhmm/IntelPDHMM.java | 4 0 + 4 - 0 !
src/main/java/com/intel/gkl/smithwaterman/IntelSmithWaterman.java | 2 0 + 2 - 0 !
src/main/native/pairhmm/IntelPairHmm.cc | 11 0 + 11 - 0 !
src/main/native/pairhmm/IntelPairHmm.h | 8 0 + 8 - 0 !
src/main/native/pdhmm/IntelPDHMM.cc | 5 0 + 5 - 0 !
src/main/native/pdhmm/IntelPDHMM.h | 2 0 + 2 - 0 !
src/main/native/pdhmm/pdhmm-implementation.h | 5 0 + 5 - 0 !
src/main/native/smithwaterman/IntelSmithWaterman.cc | 9 0 + 9 - 0 !
src/main/native/smithwaterman/IntelSmithWaterman.h | 8 0 + 8 - 0 !
10 files changed, 57 deletions(-)

 removing calls to donenative methods, which are empty and cause
 UnsatisfiedLinkError in the tests.

CMakeLists.txt | 2 1 + 1 - 0 !
src/main/native/compression/otc_zlib/CMakeLists.txt | 2 1 + 1 - 0 !
2 files changed, 2 insertions(+), 2 deletions(-)

 raising cmake minimum required version as current numbers are
 deprecated using the current CMake version in Debian