Add a new option to use a directory as output destination

[r78v10a07]

New feature to be added

[vmkalbskopf]

This is an extremely important feature if you use docker to run TPMCalculator. All of the files created by it will be in the root directory, not the mounted volume, so as soon as the container ends, all of the files are gone.

I got around it by running a script of TPMCalculator where /mnt/ is the internal mount point:

cd /mnt/
TPMCalculator -g /mnt/gencode44/chr21.gtf  -b /mnt/chr21.bam