Feature Read Per Gene

As mentioned earlier, this is the code to make the pipeline also produce gene read count files. I also changed the output count file names to disambiguate each of them (since we know have gene base counts and gene read counts).

In addition to this, the toolbox python should also be updated, since the tool used to count the reads per gene (HTSeq) is actually a Python package. Let me know if you need any help with this.

Also, of course some test runs should be done :).