GFF and SAM test files plus test helper added
We need exact match here. Explained in description

Looking for example at a gff file form chado, we would end up no being
able to distinguish between a  gene id = GreatCurl and a CDS id =
GreatCurl.1:exon:1
Exact match was definitely needed here.
I opted for doing exact match for the header as well.
Replaced polypeptide with gene

Gene feature is now taken into account. Polypetide is not needed.
This is not complete yet. We have to make a decision before this step
as to what we consider the main GFF feature (Gene / CDS /exon). It's
one step closer though.
Added test name to 2d test array

Easier to see at what stage code is at
Overlapping tests not passing

Will need to create a more controlled test for the overlapping genes to
understand what's going on
Overlapping feature tests are no correct

Essentially, I had the SAM flag on the Overlapping_Features and
Overlapping In Different frames of translation SAM files set to 4
(unmapped reads) and as expected the code wasn't counting these reads
at all. I changed the flag to 0 and now the reads are picked up.
Sense/Antisense-Forward/Reverse tests

Not all yet, but getting there.
Changed the names of files and test descriptions

It's more correct from the biological concepts point of view
Strand Specific tests in place
Paired Reads Mapping test
New test helper created. Splitting tests...

To diff files
Removed multiple name attributes for one feat
Removed double hash signs
Removed double hash signs
Changed phase form 0 to 2
Debug option and mammal tests
Testing for presence of undesired features
Split reads tests moved + mammal tests added
Reads are being counted properly. Tests pass
Redirecting samtools messages to dev null