Add embl output file mapping location of each core gene in the core genome alignment

[EpiDemos82]

This is not an issue, just a request for a future release. It would be great if there was an additional output embl that mapped the core genes to the core_gene_alignment.aln file. Alternatively, this could be output in the gene_presence_absence.csv (e.g. core gene = yes/no, position in aln = 1..1469).

[andrewjpage]

Sorry forgot to mention that this has been added in #218
so there is now an extra file with the coordinates.