[ADAM-416] Removing 'ADAM' prefix

Includes renames for:
* ADAMFeaturesContext class/object.
* ADAMNucleotideContigFragmentContext/RDDFunctions
* ADAMPileupContext/RDDFunctions and ADAMRODRDDFunctions
* AlignmentRecordContext, AlignmentRecordRDDFunctions
* Variation/GenotypeContext

ADAMContext, ADAMRDDFunctions, ADAMVCFInput/OutputFormats, ADAMMetric*,
and ADAMPredicate were all intentionally left unchanged.

Some method names were also changed, to remove the 'adam' prefix as a
particle within the name.
Merge pull request #418 from tdanford/remove-adam-prefix

[ADAM-416] Removing 'ADAM' prefix
[ADAM-423] Sanitize Avro strings when converting back to SAM.
[ADAM-424] Fix attempts to realign indels when there is no consensus.
[ADAM-425] Skip realignment if no targets are found.
[ADAM-426] Add ability to override indel realigner defaults.
Merge pull request #427 from fnothaft/indel-realigner-errors

Fixes for indel realigner issues
[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:
Stores original position and original cigar during realignment.
Addresses issue #348 in the adam project.