Fix Contig Length Detection for GFF Parsing

[JeanMainguy]

This PR fixes the bug reported in issue #299.

Problem Description

When parsing a GFF file, the contig length is usually extracted from the line:

##sequence-region <contig name> 1 <end position>

This length is used to adjust gene coordinates that overlap the contig edge, splitting such genes into two parts to ensure they remain within the contig boundaries (as introduced in PR #206).

However, this line is optional according to the GFF3 specification. As a result, when this line is missing, the contig length is undefined, causing errors during the correction of overlapping gene coordinates.

Solution

To resolve this issue, the correction of overlapping gene coordinates is now performed only after defining the contig length through one of these methods :

1. Primary check: Extract the contig length from the GFF file if the ##sequence-region line is present.
2. Fallback check: Parse the contig length from the FASTA sequences, whether embedded in the GFF file or provided as an external FASTA file.

If no FASTA sequence is provided, the coordinate correction step is skipped. This omission does not pose a problem since the correction is primarily necessary when extracting gene sequences from the FASTA file.