What is the significance of lower case letters?
libSlice generates what is know as extended ambiguity codes, which is the set of IUPAC codes, plus one additional code for each IUPAC code to represent the IUPAC code plus gap, ie (A-) is ‘a’, and (AC-) is ‘m’. This treats ambiguities with gaps the same as ambiguities with other bases. Lowercase letters were chosen so that there would be an obvious mapping back to IUPAC codes. If you have scripts that search for ambiguities based strictly on the case of the letter, you will need to update your script to also search for the uppercase alphabet of IUPAC ambiguity codes, or search for quality class 22, which is used to indicate ambiguous slices.
