From 4f52395795d33adaa80df969a8280f9f01254256 Mon Sep 17 00:00:00 2001
From: Ron Levine <rlevine@broadinstitute.org>
Date: Fri, 6 Jan 2017 22:16:35 -0500
Subject: [PATCH] Synchronize modification/access to
 practicalAlleleCountForPloidy

---
 .../haplotypecaller/HaplotypeCallerGenotypingEngine.java        | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
index 2a57c09ac..5e5592e6f 100644
--- a/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
+++ b/protected/gatk-tools-protected/src/main/java/org/broadinstitute/gatk/tools/walkers/haplotypecaller/HaplotypeCallerGenotypingEngine.java
@@ -353,7 +353,7 @@ public class HaplotypeCallerGenotypingEngine extends GenotypingEngine<AssemblyBa
      *  @param ploidy        ploidy of the sample
      * @param alleleMapper  original allele to haplotype map
      */
-    private VariantContext removeAltAllelesIfTooManyGenotypes(final int ploidy, final Map<Allele, List<Haplotype>> alleleMapper, final VariantContext mergedVC) {
+    private synchronized VariantContext removeAltAllelesIfTooManyGenotypes(final int ploidy, final Map<Allele, List<Haplotype>> alleleMapper, final VariantContext mergedVC) {
 
         final int originalAlleleCount = alleleMapper.size();
         practicalAlleleCountForPloidy.putIfAbsent(ploidy, GenotypeLikelihoodCalculators.computeMaxAcceptableAlleleCount(ploidy, maxGenotypeCountToEnumerate));