Change how method get_genes handle end position

[jpjarnoux]

Previously, get_genes handled the last position to agree with Python list slicing syntax, i.e., if the begin was 0 and the end was 5, get_genes returned genes at positions 0, 1, 2, 3, and 4. In the PPanGGOLiN algorithms, the syntax was known, and the results were what was expected.

However, we judged that was not the intended behavior of the method. So now, get_genes includes the gene in the position end. Also, an argument outrange_ok (boolean = False by default) was added to prevent some out-of-range index errors.

[axbazin]

I think this is all good, but I'd like to integrate the "functional_tests" branch before merging this, as this change is at the core of ppanggolin and it will be much easier to verify that there is no unexpected effects with it

[jpjarnoux]

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