Update README and cleanup top-level cli help text
Merge pull request #81 from bigdatagenomics/matt-cleanup

Update README and cleanup top-level cli help text
Fixes to pileup code.
Added function for building variant context from genotypes.
Adding indel realignment transform.

Composed of several steps:
* Targets for realignment are generated
* Realignment candidates are generated using the reads at the target site
* If candidates lead to a sufficient improvement, reads are realigned
Merge pull request #88 from bigdatagenomics/variant-context-from-genotypes

Added function for building variant context from genotypes.
Merge pull request #86 from bigdatagenomics/pileup-reference-position

Fixes to pileup code