Fix foreach block for vcf ingest
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
[ADAM-462] Coverage region calculation

This commit includes an new class, Coverage, which contains methods for
calculating coverage RDDs from RDDs of Region values.

Also included is a helper class, the PairingRDD class, which calculates
simple 'sliding' and 'pair' methods on sorted RDDs using the
"zipWithIndex trick."

(Joint work with Carl Yeksigian.)