added ReferenceMapping for Genotype

added filterByOverlappingRegion for GenotypeRDDFunctions
Merge pull request #470 from erictu/master

added ReferenceMapping for Genotype, filterByOverlappingRegion for GenotypeRDDFunctions
Reverting README.md back to 17d1d4d7d2e302c5dc4b9ba8e09e24fb9b8a48fb.
[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.