Fixed problem with pandoc ignoring formatting

This was dealt with by using only using pandoc to format the bibliography then adding
the header info and running pdflatex which does recognise it.

I also modified the header to work with A4 paper and changed the font to 12 pt
Modified to explicitly specify greek characters rather than relying on Unicode

This required a substantial rewrite of the main loop because pandoc keeps messing
up my LaTex tags.

Pandoc is now run on a completely minimal version of the text to format the references
and then all of the additional control statements are added before running pdflatex

This has the added advantage that \textit tags aren't being converted to \emph, which
means that names will continue to be italicised regardless of how \emph is displayed
first commit
modified get_taxid to return an integer rather than a string
modified test_get_taxid to test for GI numbers as input