Add SplitBam
Update stats baseQC to have percent vs count.  Rename the percent results to have Percent in the name and the count ones to no longer have Sum.  Also add a summary stat option
Update stats to write the summary statistic to stderr instead of the baseqc file to allow it to separate it from the other base info and to allow it to be written without writing all the other summary information
Stats - add --baseSum to usage
Update Stats BaseQC Summary header to be more descriptive that the mean is the first row and the standard deviation is the 2nd row
Update ClipOverlap to add some statistics output on the clips
Update ClipOverlap to have an option to only print pairs that are clipped.
Add a gapInfo tool that prints information on gaps between read pairs
Update GapInfo to add the chromosome and optionally print out the NotFirst and Reverse
Update GapInfo to by default just provide a gap width summary
Update GapInfo to check for strand when both pairs start at the same position
Update convert and writeRegion to have the option to left shift the cigar
Update the usage
Update SplitBam printouts to not have capital BAM
Update to accept splitBAM or splitBam
Add trimBam
Add polishBam and rgMergeBam
Add Orig version of the deduper
Update Dedup to remove clipping options since there were some bugs in there
Add initial version of recalibration does not compile