ArrayIndexOutOfBoundsException reported in TandemRepeat.getNumTandemRepeatUnits()

[droazen]

A user reports in https://gatk.broadinstitute.org/hc/en-us/community/posts/21559395629723-haplotycaller-alleles-arrayIndexOutofBoundsException that they are running into an edge-case ArrayIndexOutOfBoundsException in TandemRepeat.getNumTandemRepeatUnits() while running HaplotypeCaller in --alleles mode to re-genotype a 175bp deletion:

java.lang.ArrayIndexOutOfBoundsException: arraycopy: source index -26 out of bounds for byte[355]
       at java.base/java.lang.System.arraycopy(Native Method)
       at java.base/java.util.Arrays.copyOfRange(Arrays.java:3823)
       at org.broadinstitute.hellbender.tools.walkers.annotator.TandemRepeat.getNumTandemRepeatUnits(TandemRepeat.java:54)
       at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.AssemblyRegionTrimmer.trim(AssemblyRegionTrimmer.java:189)
       at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCallerEngine.callRegion(HaplotypeCallerEngine.java:656)
       at org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller.apply(HaplotypeCaller.java:271)
       at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.processReadShard(AssemblyRegionWalker.java:200)
       at org.broadinstitute.hellbender.engine.AssemblyRegionWalker.traverse(AssemblyRegionWalker.java:173)
       at org.broadinstitute.hellbender.engine.GATKTool.doWork(GATKTool.java:1098)
       at org.broadinstitute.hellbender.cmdline.CommandLineProgram.runTool(CommandLineProgram.java:149)
       at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMainPostParseArgs(CommandLineProgram.java:198)
       at org.broadinstitute.hellbender.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:217)
       at org.broadinstitute.hellbender.Main.runCommandLineProgram(Main.java:160)
       at org.broadinstitute.hellbender.Main.mainEntry(Main.java:203)
       at org.broadinstitute.hellbender.Main.main(Main.java:289)

They also report that when they increase the --assembly-region-padding from the default 100, to 150, the problem resolves.