Any way to help speed up CRAQ?

[SAMtoBAM]

Hi there!

I was wondering if you have any suggestions for speeding up CRAQ
Obviously increasing threads should help but i've essentially maximised this and looking for alternatives

I've made a pull request just to add multithreading to the samtools depth step but that improvement will be minimal ( #33 )

For my cases I am only interested in the S-AQI and R-AQI stats from here ./craq/runAQI_out/out_final.Report

Thanks for your help!