GATK 3.2-2 bug: ConcurrentModificationException

Hi,

I encountered a ConcurrentModificationException on several bam files using HaplotypeCaller 3.2-2 that ran just fine on 3.1 using the same number of threads. Here is the stack trace:

java.util.ConcurrentModificationException
    at java.util.LinkedHashMap$LinkedHashIterator.nextEntry(LinkedHashMap.java:390)
    at java.util.LinkedHashMap$EntryIterator.next(LinkedHashMap.java:409)
    at java.util.LinkedHashMap$EntryIterator.next(LinkedHashMap.java:408)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.addMiscellaneousAllele(HaplotypeCallerGenotypingEngine.java:292)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:255)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:941)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:218)
    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:708)
    at org.broadinstitute.gatk.engine.traversals.TraverseActiveRegions$TraverseActiveRegionMap.apply(TraverseActiveRegions.java:704)
    at org.broadinstitute.gatk.utils.nanoScheduler.NanoScheduler$ReadMapReduceJob.run(NanoScheduler.java:471)
    at java.util.concurrent.Executors$RunnableAdapter.call(Executors.java:471)
    at java.util.concurrent.FutureTask$Sync.innerRun(FutureTask.java:334)
    at java.util.concurrent.FutureTask.run(FutureTask.java:166)
    at java.util.concurrent.ThreadPoolExecutor.runWorker(ThreadPoolExecutor.java:1110)
    at java.util.concurrent.ThreadPoolExecutor$Worker.run(ThreadPoolExecutor.java:603)
    at java.lang.Thread.run(Thread.java:722)

And here are the program args for one of them: Program Args: -T HaplotypeCaller -R human_genome/human_g1k_v37.fasta -I <my_bam> -ERC GVCF -nct 16 --dbsnp /tmp/4437712/dbsnp_135.b37.vcf --variant_index_type LINEAR --variant_index_parameter 128000 -o /tmp/4437712/<my_sample>.vcf.gz

Let me know if you need more information.