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.
Fixing issues with writing BAMs to standard input for external read call.
Merge pull request #81 from fnothaft/pipe-fixes

Fixing issues with writing BAMs to standard input for external read call
Fixed IO deadlock when running SNAP as a read frontend.
Merge pull request #82 from fnothaft/snap-fixes

Fixed IO deadlock when running SNAP as a read frontend.
Updating for move over to the bdg-formats repository.
Merge pull request #83 from fnothaft/update-bdg-formats

Updating for move over to the bdg-formats repository.
Fixing read group code after #285 merged in adam upstream.
Merge pull request #84 from fnothaft/update-rgdictionary

Fixing read group code after #285 merged in adam upstream.
Fixing dependency issues due to injection of javax.servlet.
Merge pull request #85 from fnothaft/exclude-dependencies

Fixing dependency issues due to injection of javax.servlet.
Cleaning up avocado build.
Merge pull request #87 from fnothaft/cleanup-build

Cleaning up avocado build.