SSE compilation warning.
2. Added code to dynamically select between AVX, SSE4.2 and normal C++ (in
that order)
3. Created multiple files to compile with different compilation flags:
avx_function_prototypes.cc is compiled with -xAVX while
sse_function_instantiations.cc is compiled with -xSSE4.2 flag.
4. Added jniClose() and support in Java (HaplotypeCaller,
PairHMMLikelihoodCalculationEngine) to call this function at the end of
the program.
5. Removed debug code, kept assertions and profiling in C++
6. Disabled OpenMP for now.
mghodrat
mozdal
Karthik Gururaj