[maven-release-plugin] prepare release adam-parent-0.12.1
[maven-release-plugin] prepare for next development iteration
[ADAM-324] Adding documentation for commit/issue nomenclature and rebasing.
Merge pull request #325 from fnothaft/issue-docs

Adding documentation for commit/issue nomenclature and rebasing
[ADAM-326] Adding a 5-second retry on the HttpRangedByteAccess test.

The AMPLab webserver that is used in the test occasionally hangs?  If so, we catch
the HttpHostConnectException that the Apache lib throws, wait five seconds, and try
once more.
Merge pull request #328 from genomebridge/adam-326

[ADAM-326] Adding a 5-second retry on the HttpRangedByteAccess test.
[ADAM-294] Replacing shade plugin with appassembler.
[ADAM-316] Adding native Java language bindings for ADAM.
Reformatting pom's to match Maven's 2 space indent convention (see http://maven.apache.org/developers/conventions/code.html)
[ADAM-318] Added code coverage capture via scoverage.
add count of mismatches to mdtag
Merge pull request #329 from hammerlab/mdtag-counts

Add count of mismatches to mdtag
Added the TrackedLayout class.
Added filterByOverlappingRegion to AdamRDDFunctions
Added the VizReads tool to CLI.

VizReads is a tool for interactive or static visualization of aligned reads along the genome.
Ran ./scripts/format-source
Local static browser
Half-baked visualization
Added scalatra