added time function to output file, switched to gi format

output files now add a timestamp

files used for reference are the 'lcl|scaffoldX' style
improved regex pattern matching for Cbir gene names

some of the older regex patterns only worked for simple numerical
versions of the cbir ids. The new regex works for the more
complex pseudogene id names (eg 'CbirOR13_N(P)').
improved bed2gtf creation

also added method to Gff objects allowing return of nearest splice
junction to a locus