New pileup and faster print command

NEW FEATURES

  New pileup command that creates a reference-ordered data file sorted
  by position with the reference base and pileup (including phred scores)
  at each position

IMPROVEMENTS

  The print command is simplified and no longer launches a map-reduce job.
  Contents of files are now immediately streamed to console.

  Added the unique record group identifier to ADAM read records

BUG FIXES

  Fixed the read file format to use 0-based (instead of 1-based) offsets
  for read positions. All ADAM files are 0-based.