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
Adding scripts for publishing scaladoc.
Merge pull request #319 from fnothaft/publish-scaladoc

Adding scripts for publishing scaladoc.
[REMOVE ME] A missing 'index' argument to the Features2ADAM CLI was causing an error when running that command.

Simplifying two map arguments, where we don't need the '_'
Stub Gene, Transcript, Exon classes.