build.gradle | 106 15 + 91 - 0 !
1 file changed, 15 insertions(+), 91 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);
                            ^