bugs to be addressed

[FerriolCalvet]

This issue will serve as a compilation of bugs that need to be addressed.

• We get an error when custom annotation is activated but there is no intersection between the custom regions and the panels, fix this by making the added_regions output file as optional (assess if this has any downstream implications)
• Remove definition of VAF_distortion_sq since it does not make much sense and it is not used
• fix repetitive_mapping_variant filter