Test out the preview version of the next GKL (DO NOT MERGE)

.gitignore

@@ -35,7 +35,7 @@ funcotator_tmp
 #Eclipse files
 /bin/
 .project
-*.jar
+#*.jar
 
 #JENV local file
 .java-version

build.gradle

@@ -238,7 +238,10 @@ dependencies {
  // Library for configuration:
  implementation 'org.aeonbits.owner:owner:1.0.9'
 
- implementation 'com.github.broadinstitute:picard:' + picardVersion
+ implementation ('com.github.broadinstitute:picard:' + picardVersion) {
+ exclude module: 'gkl'
+ }
+
  externalSourceConfiguration 'com.github.broadinstitute:picard:' + picardVersion + ':sources'
  implementation ('org.genomicsdb:genomicsdb:' + genomicsdbVersion) {
  exclude module: 'log4j-api'
@@ -329,9 +332,10 @@ dependencies {
  implementation('com.github.fommil.netlib:netlib-native_system-linux-x86_64:1.1:natives')
  implementation('com.github.fommil.netlib:netlib-native_system-osx-x86_64:1.1:natives')
 
- implementation('com.intel.gkl:gkl:0.8.11') {
- exclude module: 'htsjdk'
- }
+// implementation('com.intel.gkl:gkl:0.8.11') {
+// exclude module: 'htsjdk'
+// }
+ implementation files('libs/gkl-2024_08_13.jar')
 
  implementation 'org.broadinstitute:gatk-bwamem-jni:1.0.4'
  implementation 'org.broadinstitute:gatk-fermilite-jni:1.2.0'

src/main/java/org/broadinstitute/hellbender/tools/walkers/haplotypecaller/PDPairHMMLikelihoodCalculationEngine.java

@@ -14,10 +14,7 @@
 import org.broadinstitute.hellbender.utils.genotyper.*;
 import org.broadinstitute.hellbender.utils.haplotype.Haplotype;
 import org.broadinstitute.hellbender.utils.haplotype.PartiallyDeterminedHaplotype;
-import org.broadinstitute.hellbender.utils.pairhmm.LoglessPDPairHMM;
-import org.broadinstitute.hellbender.utils.pairhmm.PDPairHMM;
-import org.broadinstitute.hellbender.utils.pairhmm.PairHMM;
-import org.broadinstitute.hellbender.utils.pairhmm.PairHMMInputScoreImputator;
+import org.broadinstitute.hellbender.utils.pairhmm.*;
 import org.broadinstitute.hellbender.utils.read.GATKRead;
 import org.broadinstitute.hellbender.utils.read.ReadUtils;
 
@@ -114,7 +111,7 @@ public PDPairHMMLikelihoodCalculationEngine(final byte constantGCP,
  this.log10globalReadMismappingRate = log10globalReadMismappingRate;
  this.pcrErrorModel = this.dragstrParams == null ? pcrErrorModel : PairHMMLikelihoodCalculationEngine.PCRErrorModel.NONE;
  // TODO later we probably need a LOG and LOGLESS version for parsimony with DRAGEN
- this.pdPairHMM = new LoglessPDPairHMM();
+ this.pdPairHMM = new VectorLoglessPairPDHMM(VectorLoglessPairPDHMM.Implementation.OMP , new PairHMMNativeArguments());
  if (resultsFile != null) {
  pdPairHMM.setAndInitializeDebugOutputStream(new OutputStreamWriter(resultsFile.getOutputStream()));
  }

src/main/java/org/broadinstitute/hellbender/utils/pairhmm/PDPairHMM.java

@@ -50,6 +50,12 @@ public enum Implementation {
  logger.info("Using the non-hardware-accelerated Java LOGLESS_CACHING PairHMM implementation");
  return hmm;
  }),
+ /* Optimized version of the PairHMM which caches per-read computations and operations in real space to avoid costly sums of log10'ed likelihoods */
+ AVX_LOGLESS_CACHING(args -> {
+ final PDPairHMM hmm = new VectorLoglessPairPDHMM(VectorLoglessPairPDHMM.Implementation.OMP, args);
+ logger.info("Using the non-hardware-accelerated Java LOGLESS_CACHING PairHMM implementation");
+ return hmm;
+ }),
  FASTEST_AVAILABLE(args -> {
  return new LoglessPDPairHMM();
  });
@@ -120,7 +126,7 @@ public void initialize( final List<PartiallyDeterminedHaplotype> haplotypes, fin
  initialize(readMaxLength, haplotypeMaxLength);
  }
 
- private static int findMaxAlleleLength(final List<? extends Allele> alleles) {
+ static int findMaxAlleleLength(final List<? extends Allele> alleles) {
  int max = 0;
  for (final Allele allele : alleles) {
  final int alleleLength = allele.length();