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HaplotypeCaller does not output reference haplotype in bamout
I am using HC in GATK v3.2-2-gec30cee and trying to visualize the locally reassembled reads in IGV. For one sample, which is hetRA, the bam file produced by -bamout shows the reads and the variant as expected. For another which is called as homRR in this position, I don't see any reads at all, although MIN_DP in this block is 26 according to GVCF. Also viewing the input bam to HC shows a bunch of reads supporting the reference allele.
I tried using -AR and -forceActive to ensure the locus is processed, and different options for bamWriteType and output_mode. Still no success in getting the assembled reads in the bamout file. When running with the -debug flag, I can see that the site is processed and called homRR ("Found only the reference haplotype in the assembly graph"), but no reads are printed to the bamout. Is this the intended behaviour? Is there a way of getting these reads out into the bamout file?