Issue #19 Change references from ADAMFastaNucleotideContig to ADAMNucleotideContig
Merge pull request #20 from arahuja/removefasta

Issue #19 Change references from ADAMFastaNucleotideContig to ADAMNucleo...
Build changes for new schema
Merge pull request #22 from hammerlab/build-with-new-schema

Build changes for new schema
genotype calculation inverted
Merge pull request #23 from hammerlab/fix-genotype-likelihoods

[WIP] Genotype likelihood calc was flipped
Two changes: Update to build against ADAM 0.7.1-SNAPSHOT and remove dependency versions from being specified twice
Merge pull request #24 from hammerlab/build-with-new-schema

Two changes: Update to build against ADAM 0.7.1-SNAPSHOT
Update README.md

Reflects that a local install of ADAM is no longer needed.
Adding configurable input stage to pipeline.
Updating to point to ADAM 0.7.2 snapshot release.
Merge pull request #26 from bigdatagenomics/adam-0.7.2

Updating to point to ADAM 0.7.2 snapshot release.
Merge pull request #21 from bigdatagenomics/input-stage

Adding configurable input stage to pipeline.
Updated variant callers to remove variant type field, as it has been removed in ADAM.
Merge pull request #29 from fnothaft/remove-variant-type

Merge PR #29: Updated variant callers to remove variant type field, as it has been removed in ADAM
Remove lingering references to VariantType, which was removed from ADAM
Merge pull request #30 from hammerlab/remove-lingering-VariantType

Remove lingering references to VariantType, which was removed from ADAM
Remove ReadModifier.scala, which appears to be dead code.
Merge pull request #32 from hammerlab/remove-read-modifiers

Remove ReadModifier.scala, which appears to be dead code.
change config and avocado main for basic run