fix: structure-generator takes regions other than exons into account

[balajtimate]

Describe the bug
Currently, structure-generator uses regions other than exons (like CDS, start_codon, five_prime_utr etc) to generate the output intron/exon structures, leading to a result of more exons in the output than in the input gtf file.

The tool also checks whether the output files already exist, and runs to an error if they do. This is not a problem in the Nextflow pipeline, but it would be beneficial to remove this check for faster testing the tool on its own.

Expected behavior
Structure-generator should filter the input gtf to only make use of the entries labeled as exons.

Also add the functionality to override the output files for faster testing.