Fixing sources jar
Making the CredentialsProperties file optional
Merge pull request #313 from genomebridge/credentialsPropertiesOption

Making the CredentialsProperties file optional
Merge pull request #312 from genomebridge/sources-jar

Fixing sources jar
Added table of (wall-clock) stage durations when the print_metrics option is used

The ADAMMetricsListener now records the wall-clock duration of each Spark stage. Previously only the total time taken for all of the tasks in the stage was recorded, but this is different from the wall-clock time on a multiple node cluster.

Also changed the text of the print_metrics option to clarify that metrics are printed to the log (as opposed to stdout)
Merge pull request #315 from nfergu/stage-metrics

Added table of (wall-clock) stage durations when print_metrics is used
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.
Use the scala.Console.out rather than System.out in PrintADAM

This seems to allow us to (in tests) redirect the output stream using the
Console.withOut command.
Added a failing test for Features2ADAM

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.
Added the missing 'index' argument to the Features2ADAMArgs class

Fixes the bug tested in the previous commit.