Updating pileup conversion code to convert sequences that use the X and = (EQ) CIGAR operators.
Merge pull request #199 from fnothaft/pileup-xeq

Updating pileup conversion code to convert sequences that use the X and = (EQ) CIGAR operators
Identifier consistency & formatting cleanup Issue #126

The commits fix issue #162.

Adam --> ADAM for all file contents and file names.
All scala code reformatted with https://github.com/mdr/scalariform/wiki/Command-line-tool
Move package from edu.berkeley.cs.amplab to org.bdgenomics
Merge pull request #203 from massie/package-move

Move package from edu.berkeley.cs.amplab to org.bdgenomics
[maven-release-plugin] prepare release adam-parent-0.8.0
[maven-release-plugin] prepare for next development iteration
[maven-release-plugin] prepare release adam-parent-0.8.0
[maven-release-plugin] rollback the release of adam-parent-0.8.0
[maven-release-plugin] prepare release adam-parent-0.8.0
Revert "[maven-release-plugin] prepare release adam-parent-0.8.0"

This reverts commit 9d0382503dafecee9c970d91d44e945068fba4f4.
[maven-release-plugin] prepare release adam-parent-0.8.0
[maven-release-plugin] prepare for next development iteration
Revert the pom updates to 0.8.x
[maven-release-plugin] prepare release adam-parent-0.8.0
[maven-release-plugin] rollback the release of adam-parent-0.8.0
[maven-release-plugin] prepare release adam-parent-0.8.0
[maven-release-plugin] prepare for next development iteration
Fixup the changelog script and update CHANGES.md
Small update to the release instructions