Added argument handling (-km flag) for key modification and logic to
decide if the modification was requested

Added argument handling for determining how to handle barcode / indicies
(-wiid flag)
New method noBarcodeKeyParseReadIntoTagAndTaxa that doesn't check for
barcodes because they don't exist and instead uses the cut site as an
identifier

New method to set the cut site as the id, setCutSiteAsID.  

Trimmed logic for checkForCutSite so that as long as the cut site is
found, it's position is reported
removed whitespace
Added two flags to argument fields, one checks if the user wants to be
able to modify the 2nd barcode file, the other is used to determine how
and where the user is identifying their forward and reverse sequences
(via barcode files, enzymes, Illumina tags)

set up switch logic to handle first two cases (barcodes for each read,
barcode for forward read - enzyme for reverse)
In progress, adding new flags and different parsing options
debugging
debug
debugging
Beginging to restructure CLI options to wiid and Ns present in read 1
and read 2 to lessen the options the user has to choose from when
sending the command.  Started created the new nested switch structure.
added new flag options to help narrow the user's input without
overloading them with fixed options.
2013-05-15