No option to have KINgaroo intermediate files anywhere but the running folder

[gilibean]

Hello ,
I have noticed that KINgaroo is creating intermediate files in folders: hapProbs, splitbams and hbd_results, which are created automatically in the folder the program is being run.

This is problematic for several reasons.

1. there may not be enough space on the running directory.
2. if you cannot control where you run the program (and I can't because I use a multi-servers queuing system), it is not possible to run several instances of the program at the same time. This has proven to be a big problem because I couldn't test different parameters at the same time, and KINgaroo run may take several days to complete. In addition, I cannot try the program over several different families at the same time (theoretically, it is possible if the .bam names are different, but since you are deleting intermediate files at the end of the run, I cannot tell if parallel runs wouldn't interfere with each other.

Generally, I don't think it is healthy to create intermediate files just at a random folder that the user has no control over. Please change this so I can continue using your software and test for Kinship.
Thank you!