added cropping functions to main script

Lotti, I have:

added the call to your cropseq function to the main script
inserted gaps to make up for the cropped regions
added logging (but I've not completely checked the logged numbers are right yet)
added a parameter to set the minimum size gap to base the cropping on in the findValue function
added a "keep gaps" option to the consensus - so that you can use only positions where the most common base isn't a gap.
added a remove gap only sites function

KatyBrown / CIAlign