Allow User to Set Custom E-value Threshold and Include E-value in Summary Table Description:

[konstytucja]

It would be beneficial for users to have the ability to manually set the E-value threshold. Currently, I think it is arbitrarily set to 10^-3 in the code. Additionally, I believe it would be valuable to include information about these E-value thresholds in the final_genes_to_contigs_annotation_summary.tsv table.

Benefits:

• Enhanced flexibility for users to customize their analysis.
• Improved transparency and completeness of the summary table.

[mtisza1]

Thank you for opening this issue.

There are actually different e-values for different databases, to align with the best sensitivity/specificity for each. I'm somewhat against allowing users to modify so that results are consistent. But your point is taken that this could be documented. I'll plan to add this somewhere.