[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.
[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.)