Fix foreach block for vcf ingest
Documentation cleanup and style improvements
Merge pull request #492 from massie/doc-cleanup

Documentation cleanup and style improvements
Merge pull request #494 from kyocum/fixVcfIngest

Fix foreach block for vcf ingest
[ADAM-473] Make RecordCondition and FieldCondition public

Fixes #473
Merge pull request #503 from laserson/ADAM-473

[ADAM-473] Make RecordCondition and FieldCondition public
[ADAM-502] Add missing Long implicit to ColumnReaderInput

Fixes #502
Merge pull request #504 from laserson/ADAM-502

[ADAM-502] Add missing Long implicit to ColumnReaderInput
[ADAM-505] Removed `adam-local` from docs
Merge pull request #507 from laserson/ADAM-505

[ADAM-505] Removed `adam-local` from docs
[ADAM-499] Add -onlyvariants option to vcf2adam

Fixes #499.
Merge pull request #501 from laserson/ADAM-499

[ADAM-499] Add -onlyvariants option to vcf2adam
[ADAM-495] Require SPARK_HOME for adam-submit

Also 2 tiny cosmetic changes for the other scripts.

Fixes #495.
Merge pull request #500 from laserson/ADAM-495

[ADAM-495] Require SPARK_HOME for adam-submit
[ADAM-496] Changes VCF to flat ADAM command name and usage

Fixes #496.
Merge pull request #498 from laserson/ADAM-496

[ADAM-496] Changes VCF to flat ADAM command name and usage
Upgrade from Parquet 1.4.3 to 1.6.0rc4

This upgrade adds dictionary support which dramatically reduces the
memory footprint.

For example, a simple program to load and count mouse mitochondrial DNA..

  val reads = ac.loadAlignments("/workspace/data/mouse_chrM.adam").cache()
  println(reads.count())

In 1.6.0rc4, this rdd was able to be cached in memory, e.g.

14/11/24 10:37:16 INFO BlockManagerInfo: Added rdd_1_0 in memory on zenfractal:60004 (size: 193.0 MB, free: 72.5 MB)

With 1.4.3, it was not, e.g.

14/11/24 10:33:07 WARN CacheManager: Not enough space to cache partition rdd_1_0 in memory! Free memory is 278185689 bytes.
Merge pull request #508 from massie/parquet-1.6.0

Upgrade from Parquet 1.4.3 to 1.6.0rc4
[ADAM-489] Moved Spark and Hadoop to provided dependency.
Add a 'distribution' module to create assemblies

o Moves the maven-assembly-plugin from adam-cli to the
  new distribution module
o Updates the adam-submit and friends to work from source
  or binary distributions
o Generates docs and adds them to the distribution
o Adds LICENSE, NOTICE.txt, CHANGES.md, etc to distribution