speed of running setAlleleMats step

[lixin4306ren]

Hi, thank you for providing such a useful tool.

My dataset has ~9k cells and I use all ~60k SNPs provided from HoneyBADGER package (ExAC database) to run setAlleleMats. I found running this step was very slow even it used over 10 cores in the server (it showed 7028 heterozygous SNPs identified). I then tested 9k cells only using 1 SNP with 1 core, it took over 10 minutes (I'm not sure whether it's a reasonable time). How could I speed up in this step? Thanks.