zacherydickson/HUBDesign: Version 1.6.0

Update to better handle non-prokka annotations as input:

Added new option to to clustering phase (--gene-name-regex) which manages how gene names are parses The old default behaviour of stripping off copy numbers after an underscore is no longer default This behaviour can be recovered by using '[^_]' as the argument for --gene-name-regex (or -r if using the Clustering sub command)

Minor Change to gene identifiers, previous behaviour assumed ids were unique across all taxa, this is now assured by appending the txid and an arbitrary sequential number to each gene id. Carriage returns in the input file specifying gff locations and txids are now handled