Fixed TransCount() and Updated ScanTrio()

There was an error in TransCount().  We don't need to loop through ranges in the GRanges object.  We treat each GRanges object as one window.  We do not require that the window be one range, e.g., the 'outside of window' GRange object has two ranges.  We only want to loop through elements of the GRangesList.  This is a list of GRanges objects that are to be treated as windows.
I don't think anything was actually changed.
Changed trios() to return character vectors

I am still having problems agreeing with plink, and also not observing all triostates.
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Debugged some problems

Still having trouble with the M O switch.  I don't know why but for some reason the code only generates correct results when I switch the genotpye matrixes for M and O in the GenoTrio() object.  I have no idea why this is happening, but I don't think the problem is on the data level becuase plink and SnpStats behave correctly (seemingly).
Updated ScanTrio method and created CNVTrioExperiment class

In this commit I added CNVTrioExperiment, updated show method for STE, discovered M/O bug was on the data level, and updated the ScanTrio output.  The M/O bug in the data has been corrected.  The new SNP matrices are in vcf2R package on enigma.
Fixed bug in MAF()

Also updated vignette.
Updated vignette
Updated vignette
Updated vignette
Created generator function for CNVTrioExperiment

There have already been several methods available for ste that were need for cte.  I copied and pasted for a temporary patch.  This needs to be changed so that they both inherit from the same class, or functions exist in a functions.R file that are called by both methods.  The latter makes the structure very cryptic for the reader of the source code.
Chnaged README to a link to DESCRIPTION
Updated DESCRIPTION
Updated vignette

Also removed some useless cat in TransCount().