Updates to indel realigner to improve performance and accuracy.
Adding scripts for publishing scaladoc.
Merge pull request #319 from fnothaft/publish-scaladoc

Adding scripts for publishing scaladoc.
Remove extraneous implicit methods
Merge pull request #314 from fnothaft/indel-realigner-rebase

Updates to indel realigner to improve performance and accuracy.
Merge pull request #320 from genomebridge/remove-implicit-methods

Remove extraneous implicit methods in ReferenceMappingContext
Adding code for lifting over between sequences and the reference genome.
Merge pull request #306 from fnothaft/liftover

Adding code for lifting over between sequences and the reference genome.
[ADAM-322] Adding ADAMFeatureField for projections over ADAMFeature.

For some reason, we'd neglected to include an ADAMFeatureField class in the adam.projections
package!  This commit fixes that.
[ADAM-307] Fixing Features2ADAM so that it can be run from the CLI.

Features2ADAM fails because it doesn't include an 'index' field in its
second command-line argument, and therefore Args4j can't parse the Features2ADAMArgs
object off a command line.

This commit adds the missing 'index' argument to the Features2ADAMArgs class.

There is a test for this additional feature -- however, that test is marked as IGNORE
because we can't get it to work either locally or on Jenkins.  This should be addressed,
and I'll open up a ticket for it.  In the meantime, however, we've verified that manually
that this patch works as advertised.

Also modified PrintADAM to use the scala.Console.out rather than System.out.
This seems to allow us to (in tests) redirect the output stream using the
Console.withOut command.
Merge pull request #308 from genomebridge/features2adam-bug

Fixing the 'index 0' bug in features2adam
[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