[ADAM-331] Moving code coverage analysis into a profile, so it is not packaged into artifacts.
Merge pull request #334 from fnothaft/fix-ccov

Moving code coverage into a profile
[ADAM-330] Make mismatch and deletes positions accessible
Merge pull request #330 from hammerlab/mdtag-access

Make mismatch and deletes positions accessible
[ADAM-311] Adding several simple normalizations.
Merge pull request #311 from fnothaft/simple-normalizations

Adding several simple normalizations.
[ADAM-335] Updated README.md to reflect migration to appassembler.
Merge pull request #337 from fnothaft/appassembler-update-docs

[ADAM-335] Updated README.md to reflect migration to appassembler.
[ADAM-340] Adding the TrackedLayout trait and implementation.

OrderedTrackLayout is an implementation of TrackedLayout, which takes a sequence of Reference-mappable values and lays them out into tracks in a naive, order-dependent way.
Merge pull request #341 from genomebridge/tdanford/tracked-layout

[ADAM-340] Adding the TrackedLayout trait and implementation.
[ADAM-332] Upgrades ADAM to Spark 1.0.1.
Merge pull request #333 from fnothaft/upgrade-spark

[ADAM-332] Upgrades ADAM to Spark 1.0.1.
[ADAM-309] Update to bdg-formats 0.2.0

- Some of the files have been renamed as part of the renames in
  bdg-formats
- I cleaned up some of the references in the files, as well as some of
  the IntelliJ complaints in the files
- Adding ClasspathFileLocator to allow testing local files
Merge pull request #342 from genomebridge/bdg-formats-0.2.0

[ADAM-309] Update to bdg-formats 0.2.0
Merge remote-tracking branch 'upstream/master' into vis2

Conflicts:
	adam-core/src/main/scala/org/bdgenomics/adam/models/TrackedLayout.scala
Bugging on Ordered Tracked Layout