Added documentation for pairParam class.
Changed boxPairs documentation to reflect pairParam input.
Got rid of normalize method for DIList, to avoid csaw dependency.
Fixed a bug in reform, added restrict to show for pairParam.
Invisibilized preparePairs in boxPairs example.
Modified squareCounts docs to handle pairParam input.
Modified connectCounts docs to support pairParam input.
Modified marginCounts documentation to accept pairParam input.
Modified getPairData docs to reflect pairParam input, countPairs -> prunePairs. Added some detail on insert sizes.
Added prunePairs documentation, based on old countPairs docs.
Updated mergePairs docs to reflect removal of count information from index files.
Modified totalCounts docs to reflect pairParam input.
Modified savePairs to take in pairParam object.
Modified tests to reflect new savePairs.
Added *.pos, *.len fields to example for savePairs, mentioned to look at preparePairs to see what they mean.
Updated plotPlaid and rotPlaid documentation to use pairParam objects.
Fixed bug in plotPaid, rotPlaid, and corrected warning.
Modified getArea to use (optional) pairParam inputs.
Modified getArea docs to reflect pairParam input.
Modified examples to accept pairParam input.