gatk-3.8/public/VectorPairHMM

Implementation overview: Created a new Java class called VectorLoglessPairHMM which extends LoglessPairHMM and overrides functions from both LoglessPairHMM and PairHMM.

1. Constructor: Call base class constructors. Then, load the native library located in this directory and call a global init function in the library to determine fields ids for the members of classes JNIReadDataHolder and JNIHaplotypeDataHolders.
2. When the library is loaded, it initializes two global function pointers to point to the function implementation that is supported on the machine on which the program is being run. The two pointers are for float and double respectively. This initialization is done only once for the whole program.
3. initialize(): To initialized the region for PairHMM. Pass haplotype bases to native code through the JNIHaplotypeDataHolders class. Since the haplotype list is common across multiple samples in computeReadLikelihoods(), we can store the haplotype bases to the native code once and re-use across multiple samples.
4. computeLikelihoods(): Copies array references for readBases/quals etc to array of JNIReadDataHolder objects. Invokes the JNI function to perform the computation and updates the likelihoodMap.

Note: Debug code has been moved to a separate class DebugJNILoglessPairHMM.java.

On the C++ side, the primary function called is Java_org_broadinstitute_sting_utils_pairhmm_VectorLoglessPairHMM_jniComputeLikelihoods. It uses standard JNI calls to get and return data from/to the Java class VectorLoglessPairHMM. The last argument to the function is the maximum number of OpenMP threads to use while computing PairHMM in C++. This option is set when the native function call is made from JNILoglessPairHMM computeLikelihoods - currently it is set to 12 (no logical reason). Note: OpenMP has been disabled for now.

Compiling: Make sure you have icc (Intel C compiler) available. Currently, gcc does not seem to support all AVX intrinsics. Type 'make'. This should create a library called libVectorLoglessPairHMM.so

Running: The default implementation of PairHMM is still LOGLESS_CACHING in HaplotypeCaller.java. To use the native version, use the command line argument "--pair_hmm_implementation VECTOR_LOGLESS_CACHING" (see run.sh in src/main/c++). The native library is bundled with the StingUtils jar file. When HaplotypeCaller is invoked with the VectorLoglessPairHMM implementation (see run.sh in the directory src/main/c++), then the library is unpacked from the jar file, copied to the /tmp directory (with a unique id) and loaded by the Java class VectorLoglessPairHMM in the constructor (if it has not been loaded already). The default library can be overridden by using the -Djava.library.path argument for the JVM to pass the path to the library. If the library libVectorLoglessPairHMM.so can be found in java.library.path, then it is loaded and the 'packed' library is not used. See run.sh in this directory on how to invoke HaplotypeCaller with the vector implementation of PairHMM. The argument -Djava.library.path is needed if you wish to override the default packed library, else unnecessary.