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Genomics compute kernels optimized for Intel Architecture
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package com.intel.gkl.pairhmm;

import com.intel.gkl.IntelGKLUtils;
import org.broadinstitute.gatk.nativebindings.pairhmm.HaplotypeDataHolder;
import org.broadinstitute.gatk.nativebindings.pairhmm.PairHMMNativeArguments;
import org.broadinstitute.gatk.nativebindings.pairhmm.PairHMMNativeBinding;
import org.broadinstitute.gatk.nativebindings.pairhmm.ReadDataHolder;

import java.io.File;

public class IntelPairHmm implements PairHMMNativeBinding {

    /**
     * Load native library using system temp directory to store the shared object.
     *
     * @return true if IntelPairHmm is supported on the platform
     */
    public boolean load() {
        return load(null);
    }

    /**
     * Load native library using tmpDir to store the shared object.
     *
     * @param tmpDir the directory used to store a copy of the shared object
     * @return true if IntelPairHmm is supported on the platform
     */
    @Override
    public boolean load(File tmpDir) {
        return IntelGKLUtils.load(tmpDir);
    }

    /**
     * Initialize native PairHMM with the supplied args.
     *
     * @param args the args used to configure native PairHMM
     */

    @Override
    public void initialize(PairHMMNativeArguments args) {
        initNative(ReadDataHolder.class, HaplotypeDataHolder.class, false, 100);
    }

    /**
     *
     *
     * @param readDataArray array of read data
     * @param haplotypeDataArray array of haplotype data
     * @param likelihoodArray array of double results
     */

    @Override
    public void computeLikelihoods(ReadDataHolder[] readDataArray,
                                   HaplotypeDataHolder[] haplotypeDataArray,
                                   double[] likelihoodArray)
    {
        computeLikelihoodsNative(readDataArray, haplotypeDataArray, likelihoodArray);
    }

    /**
     *
     */
    @Override
    public void done() {
        doneNative();
    }

    private native static void initNative(Class readDataHolderClass,
                                          Class haplotypeDataHolderClass,
                                          boolean doublePrecision,
                                          int maxThreads);

    private native void computeLikelihoodsNative(Object[] readDataArray,
                                                 Object[] haplotypeDataArray,
                                                 double[] likelihoodArray);

    private native void doneNative();
}