makeBed.pl fully functional
new file overlap.pl to read the output of bedtools and find in which location in protein coordinates the IES are present
overlap.pl read:
 - the output of bedtools intersect with the -wo option (which genes contain IES)
 - the .bed file with IES coordinates
 - master genbank file
and produces an output file with the following columns
 - geneId
 - IESid
 - 1-based index of IES location in aa coordinates (including start codon as M)
 - frame of insertion (counting as start the point closest to the origin of the protein, which depends on the strand of the protein) 0 1 2
fixed input/output of overlap.pl, now takes command line options and prints to files