Synchronize for reads as well as writes to shared state.

src/main/java/org/broadinstitute/hellbender/tools/walkers/genotyper/GenotypeLikelihoodCalculators.java

@@ -9,7 +9,8 @@
 import java.util.Arrays;
 
 /**
- * Genotype likelihood calculator utility.
+ * Genotype likelihood calculator utility. This class is thread-safe since access to shared mutable state is
+ * synchronized.
  *
  * <p>
  *     This class provide genotype likelihood calculators with any number of alleles able given an arbitrary ploidy and allele
@@ -257,7 +258,7 @@ private static GenotypeAlleleCounts[] buildGenotypeAlleleCountsArray(final int p
      *
      * @return never {@code null}.
      */
-    public GenotypeLikelihoodCalculator getInstance(final int ploidy, final int alleleCount) {
+    public synchronized GenotypeLikelihoodCalculator getInstance(final int ploidy, final int alleleCount) {
         checkPloidyAndMaximumAllele(ploidy, alleleCount);
 
         if (calculateGenotypeCountUsingTables(ploidy, alleleCount) == GENOTYPE_COUNT_OVERFLOW) {
@@ -270,9 +271,7 @@ public GenotypeLikelihoodCalculator getInstance(final int ploidy, final int alle
     }
 
     /**
-     * Update of shared tables. Note that this method is synchronized to avoid race conditions in Spark. This is because
-     * in Spark each region has its own HaplotypeCallerEngine instance (so there can be multiple instances in a single
-     * JVM), but these share a single (static) instance of this class (via AlleleSubsettingUtils).
+     * Update of shared tables.
      *
      * @param requestedMaximumAllele the new requested maximum allele maximum.
      * @param requestedMaximumPloidy the new requested ploidy maximum.
@@ -381,7 +380,7 @@ public static int computeMaxAcceptableAlleleCount(final int ploidy, final int ma
         throw new GATKException("Code should never reach here.");
     }
 
-    private int calculateGenotypeCountUsingTables(int ploidy, int alleleCount) {
+    private synchronized int calculateGenotypeCountUsingTables(int ploidy, int alleleCount) {
         checkPloidyAndMaximumAllele(ploidy, alleleCount);
         ensureCapacity(alleleCount, ploidy);
         return alleleFirstGenotypeOffsetByPloidy[ploidy][alleleCount];