Adding generic stub for external variant callers.
Refactoring assembler into a general haplotype based caller.
Merge pull request #77 from fnothaft/haplotype

Refactoring assembler into a general haplotype based caller.
Merge pull request #76 from fnothaft/external-call

Adding generic stub for external variant callers.
Fixing build.
Merge pull request #78 from fnothaft/fix-build

Fixing build.
Changed license header to new BDGenomics license header.
Merge pull request #80 from fnothaft/change-license

Changed license header to new BDGenomics license header.