First import of AVX-JNI to git
Changes:
1. Added TRISTATE_CORRECTION in pairhmm-template-kernel.cc (function
stripINITIALIZATION)
2. Added VEC_DIV macros to define-double.h and define-float.h
3. Edited initializeVectors to match Java
C++ original:
*(ptr_p_MY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_d];
*(ptr_p_YY+r-1) = (r == ROWS - 1) ? ctx._(1.0) : ctx.ph2pr[_c];
Modified:
*(ptr_p_MY+r-1) = ctx.ph2pr[_d];
*(ptr_p_YY+r-1) = ctx.ph2pr[_c];
1. Added support for JNI integration for LoglessCaching PairHMM AVX
implementation.
2. Contains lots of debug code
3. Only invokes JNI for subComputeReadLikelihoodGivenHaplotypeLog10
1. Nested loops over reads and haplotypes moved to C++ through JNI
2. OpenMP support added
3. Using direct access to Java primitive arrays
4. Debug messages disabled
Minor typo in comments fixed
Removed unnecessary files
Renamed directory
Merge branch 'master' of /home/karthikg/broad/archive/hmm_intra into intel_pairhmm
1. Moved computeLikelihoods from PairHMM to native implementation
2. Disabled debug - debug code still left (hopefully, not part of
bytecode)
3. Added directory PairHMM_JNI in the root which holds the C++ library
that contains the PairHMM AVX implementation. See PairHMM_JNI/JNI_README
first
Same log message as before - forgot -a option
1. Moved computeLikelihoods from PairHMM to native implementation
2. Disabled debug - debug code still left (hopefully, not part of
    bytecode)
3. Added directory PairHMM_JNI in the root which holds the C++
library that contains the PairHMM AVX implementation. See
PairHMM_JNI/JNI_README first
Uncommenting download option in build.xml
Added support for dynamic selection between AVX and un-vectorized C++,
still to include SSE code from Mohammad.
Debug flags turned on in this commit.
1. Integrated Mohammad's SSE4.2 code, Mustafa's bug fix and code to fix the
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.
1. Enabled OpenMP
2. Enabled AVX - earlier commit had disabled AVX
Fixed bug in JNI interface release_array
Disabled OpenMP
Got rid of the MMX instructions in the SSE version of the code. Handling the mask operations in a class, which is defined for each version of SSE and AVX implementations separately.
1. Inserted #define in sandbox pairhmm-template-main.cc
2. Wrapped _mm_empty() with ifdef SIMD_TYPE_SSE
3. OpenMP disabled
4. Added code for initializing PairHMM's data inside initializePairHMM -
not used yet
Split the inner loop to avoid the overhead incurred when -fPIC flag is enabled.
Merge branch 'master' of /home/mozdal/git/hmm into intel_pairhmm

Conflicts:
	PairHMM_JNI/pairhmm-1-base.cc
	PairHMM_JNI/pairhmm-template-kernel.cc
	PairHMM_JNI/utils.cc
Deleted libJNILoglessPairHMM.so from git tracking