[ADAM-429] adam-submit now handles args correctly.

Makes use of the `gatherSparkSubmitOpts` in Spark's `bin/utils.sh`. Fixes #429
Merge pull request #430 from laserson/ADAM-429

[ADAM-429] adam-submit now handles args correctly.
[ADAM-431] Several random cleanups:

- README tweak

- wrap some long lines

- clarify command parsing in ADAMMain

- quote bash var

- make `GenomicRegionPartitioner` a case class

  seems like it’s well-suited to be one:
  - public ctor vals
  - boilerplate .equals method
  - wrapper ctor that uses companion object method can go into companion
    object

- remove no-op `remapContig` function

  the “NB” comment about it being a no-op seems to be correct, afaict
Merge pull request #431 from ryan-williams/tweaks

[ADAM-431] Several random tweaks:
[ADAM-403] Remove seqDict from RegionJoin

Fixes #403.
Merge pull request #435 from laserson/ADAM-403

[ADAM-403] Remove seqDict from RegionJoin
[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:
read “OQ” attr from structured SAMRecord field

converting into and out of BAM using ADAM was dropping the “OQ” attr;
HTSJDK puts it in its own field but ADAM was looking for it in the
catch-all attributes field.
Revert "[ADAM-237] Migrate to Chill serialization libraries."

This reverts commit 39821152352e6647a244d1df24facafa53aa6923.
Bump scala from 2.10.3 to 2.10.4
Merge pull request #446 from massie/serializer

Revert "[ADAM-237] Migrate to Chill serialization libraries."
Merge pull request #449 from ryan-williams/origqual

read “OQ” attr from structured SAMRecord field
[ADAM-348] Stores original position and original cigar during realignment.
Addresses issue #348 in the adam project.
Merge pull request #417 from niranjan93/NK_schema_tags

Stores original position and original cigar during realignment.
Better null handling for isSameContig utility
Merge pull request #453 from massie/is-same-contig

Better null handling for isSameContig utility