[ADAM-439] Fix ADAM to account for BDG-FORMATS-35

Includes commit by @fnothaft: Fixed flipped index in indel realigner.

Fixes #439
Merge pull request #440 from laserson/ADAM-439

[ADAM-439] Fix ADAM to account for BDG-FORMATS-35: Avro uses Strings
[ADAM-461] Fix ReferenceRegion and ReferencePosition impl

This commit mainly does 3 things:

1. Fixes impl of `ReferenceRegion.width`.

2. Removes `Option`s from `ReferencePosition`.

3. Corrected impl of liftOver.  However, it now has different semantics: in all cases, the list of regions must be provided in genome order.

4. Simplifies structure of case classes.

Fixes #461.
Merge pull request #469 from laserson/ADAM-461

[ADAM-461] Fix ReferenceRegion and ReferencePosition impl
[ADAM-486] Add port option to viz command.
Merge pull request #487 from fnothaft/unhardcode-viz

[ADAM-486] Add port option to viz command.
[ADAM-480] Switch assembly to single goal.
Merge pull request #481 from fnothaft/run-assembly-once

[ADAM-480] Switch assembly to single goal.
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