fix: dubious end coordinates in structure generator output gtf

[ninsch3000]

The gtf output generated by structure generator doesn't seem to have correct end coordinates.

In every other line, 4 zeros seem to be appended to the end coordinate.
Investigate the structure generator module to identify what causes this behavior.

Currently, affected exons are lost in the bedtools step; Make sure they are retained after the coordinate issue has been solved. Else open a new issue for the erroneous bedtools output.