CGATOxford/UMI-tools: Rue The Whirl

Adds the new group command to group PCR duplicates and return the groups in a tagged BAM file and/or flat file format. This was motivated by multiple requests to group PCR duplicated reads for downstream processes, e,g #45, #54. Special thanks to Nils Koelling (@koelling) for testing the group command. Adds the --umi-separator option for dedup and group for workflow where umi_tools extract is not used to extract the UMI. This was motivated by #5