Adding Convey HC-1 HMM acceleration

protected/java/src/org/broadinstitute/sting/gatk/walkers/haplotypecaller/LikelihoodCalculationEngine.java

@@ -90,6 +90,9 @@ public class LikelihoodCalculationEngine {
                 pairHMM = new Log10PairHMM(false);
                 break;
             case LOGLESS_CACHING:
+		if (CnyPairHMM.isAvailable())
+		    pairHMM = new CnyPairHMM();
+		else
 		    pairHMM = new LoglessPairHMM();
                 break;
             default:
@@ -151,6 +154,8 @@ public class LikelihoodCalculationEngine {
 
     private PerReadAlleleLikelihoodMap computeReadLikelihoods( final List<Haplotype> haplotypes, final List<GATKSAMRecord> reads) {
         // first, a little set up to get copies of the Haplotypes that are Alleles (more efficient than creating them each time)
+	final BatchPairHMM batchPairHMM = (pairHMM instanceof BatchPairHMM) ? (BatchPairHMM)pairHMM : null;
+	final Vector<GATKSAMRecord> batchedReads = new Vector<GATKSAMRecord>(reads.size());
         final int numHaplotypes = haplotypes.size();
         final Map<Haplotype, Allele> alleleVersions = new HashMap<Haplotype, Allele>(numHaplotypes);
         for ( final Haplotype haplotype : haplotypes ) {
@@ -177,6 +182,10 @@ public class LikelihoodCalculationEngine {
                 readQuals[kkk] = ( readQuals[kkk] < (byte) 18 ? QualityUtils.MIN_USABLE_Q_SCORE : readQuals[kkk] );
             }
 
+	    if ( batchPairHMM != null ) {
+		batchPairHMM.batchAdd(haplotypes, read.getReadBases(), readQuals, readInsQuals, readDelQuals, overallGCP);
+		batchedReads.add(read);
+	    } else {
 		for( int jjj = 0; jjj < numHaplotypes; jjj++ ) {
 		    final Haplotype haplotype = haplotypes.get(jjj);
 		    final boolean isFirstHaplotype = jjj == 0;
@@ -186,7 +195,16 @@ public class LikelihoodCalculationEngine {
 		    perReadAlleleLikelihoodMap.add(read, alleleVersions.get(haplotype), log10l);
 		}
 	    }
-
+        }
+	if ( batchPairHMM != null ) {
+	    for( final GATKSAMRecord read : batchedReads ) {
+		final double[] likelihoods = batchPairHMM.batchResult();
+		for( int jjj = 0; jjj < numHaplotypes; jjj++ ) {
+		    final Haplotype haplotype = haplotypes.get(jjj);
+		    perReadAlleleLikelihoodMap.add(read, alleleVersions.get(haplotype), likelihoods[jjj]);
+		}
+	    }
+	}
         return perReadAlleleLikelihoodMap;
     }
 

protected/java/src/org/broadinstitute/sting/utils/pairhmm/CnyPairHMM.java

@@ -0,0 +1,59 @@
+package org.broadinstitute.sting.utils.pairhmm;
+
+import java.util.*;
+
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+
+public final class CnyPairHMM extends PairHMM implements BatchPairHMM {
+    private static class HmmInput {
+	public List<Haplotype> haplotypes;
+	public byte[] readBases;
+	public byte[] readQuals;
+	public byte[] insertionGOP;
+	public byte[] deletionGOP;
+	public byte[] overallGCP;
+    };
+
+    private static boolean loaded = false;
+    private List<HmmInput> pending = new LinkedList<HmmInput>();
+
+    static public boolean isAvailable() {
+	return true;
+    }
+
+    public void batchAdd(final List<Haplotype> haplotypes, 
+			 final byte[] readBases,
+			 final byte[] readQuals,
+			 final byte[] insertionGOP,
+			 final byte[] deletionGOP,
+			 final byte[] overallGCP) {
+	HmmInput test=new HmmInput();
+	test.haplotypes=haplotypes;
+	test.readBases=readBases;
+	test.readQuals=readQuals;
+	test.insertionGOP=insertionGOP;
+	test.deletionGOP=deletionGOP;
+	test.overallGCP=overallGCP;
+	pending.add(test);
+    }
+    
+    public double[] batchResult() {
+	HmmInput test=pending.remove(0);
+	double[] results=new double[test.haplotypes.size()];
+	for (int i=0; i<results.length; i++) {
+	    results[i]=0.0;
+	}
+	return results;
+    }
+
+    protected double subComputeReadLikelihoodGivenHaplotypeLog10( final byte[] haplotypeBases,
+								  final byte[] readBases,
+								  final byte[] readQuals,
+								  final byte[] insertionGOP,
+								  final byte[] deletionGOP,
+								  final byte[] overallGCP,
+								  final int hapStartIndex,
+								  final boolean recacheReadValues ) {
+	return 0.0;
+    }     
+}

public/java/src/org/broadinstitute/sting/utils/pairhmm/BatchPairHMM.java

@@ -0,0 +1,16 @@
+package org.broadinstitute.sting.utils.pairhmm;
+
+import java.util.List;
+
+import org.broadinstitute.sting.utils.haplotype.Haplotype;
+
+public interface BatchPairHMM {
+    public void batchAdd(final List<Haplotype> haplotypes, 
+			 final byte[] readBases,
+			 final byte[] readQuals,
+			 final byte[] insertionGOP,
+			 final byte[] deletionGOP,
+			 final byte[] overallGCP);
+
+    public double[] batchResult();
+}