[ADAM-432] Run indel realignment before BQSR.
[ADAM-433] Add ability to dump BQSR observations to CSV from CLI.
Merge pull request #434 from fnothaft/realign-before-bqsr

Few transform tweaks
[ADAM-437] random nits and cleanups:

- make scalariform allow dangling parends

  sometimes I find this to be a useful way to indicate nesting:

  throw new Exception(
      “%s %s %s %s”.format(
          foo, bar baz, boo
      )
  )

- tweak comment about read-ID suffixes in FASTQ

- wrap a few long lines

- add docs to adamFastqLoad method
Merge pull request #437 from ryan-williams/nits

[ADAM-437] random nits and cleanups:
Initial implementation of Coverage class.
Adding a PairingRDD function.