deduplicate variants called in multiple primer pools

[will-rowe]

Thinking about this in response to: artic-network/fieldbioinformatics#53

At the moment, artic-tools check_vcf will find variants in overlap regions and check for multiple copies. If only one copy is found it is marked as potential contamination and then dropped. If multiple copies are found, it is marked as a pass and all copies are kept.

It would be good to have an option added so that where multiple copies are found, they are collapsed and reported as a single var.