GATK 3.2-2 bug: NullPointerException

Hi,

I encountered a NullPointerException in 3.2-2 using the HaplotypeCaller on a BAM that run just fine on 3.1. Here is the stack trace:

java.lang.NullPointerException
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(PairHMMLikelihoodCalculationEngine.java:421)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.PairHMMLikelihoodCalculationEngine.computeDiploidHaplotypeLikelihoods(PairHMMLikelihoodCalculationEngine.java:395)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.calculateGLsForThisEvent(HaplotypeCallerGenotypingEngine.java:421)
    at org.broadinstitute.gatk.tools.walkers.haplotypecaller.HaplotypeCallerGenotypingEngine.assignGenotypeLikelihoods(HaplotypeCallerGenotypingEngine.java:257)
    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:

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 info.