Reporting 1-based index in definition header

To make things easier for people in the lab we use 1-based indexing now
in the header of the generated window file (e.g. the location of the
first 10 nucleotides in a read is 1..10)
Added option :shifted

Using :shifted in the options hash we can now shift the starting
position of nucleotide window creation. If we want to skip the first 50
nucleotides of a sequence we use { :shifted => 50 }