Start of codon correction update

[susannah-b]

Update to shiver to include CodonCorrection.sh and surrounding scripts, which correct genes from within the shiver remap consensus files, although are not yet integrated into a final full genome product. Includes basic shiver implementation which currently has an error with the init directory (can be removed or fixed as it only involves a few lines of code). Several hundred commits 'ahead' due to rebase issues - I haven't been able to resolve this but if there's anything I can adjust let me know - otherwise I'm hoping they can be resolved as the same commits exist in the upstream repo.

Please see the CodonCorrectionDoc PDF for further information on usage and current project status.