Created 3 modes for ResolveTool: makeStats, markPairs, & twoPass

Created 3 modes for ResolveTool: makeStats, markPairs, & twoPass
 * "TwoPass" mode (the initial implementation of the tool) effectively
eliminates piped BAMs as an input option, since you can't exactly rewind
stdin and start reading from the beginning.
 * To get around this, I separated the two passes into separate "modes"
(-makeStats & -markPairs), that communicate via a simple, human-readable
stats summary file. Data can then be merged, filtered, etc and piped
into each mode if you don't mind the runtime of preprocessing twice but
don't want to physically store the unresolved intermediate BAM file.