Adding reference assembly name to ADAMContig.
Merge pull request #262 from fnothaft/add-assembly-to-contig

Adding reference assembly name to ADAMContig.
Adding an 'args' parameter to the plugin framework.

PluginExecutor now takes a plugin_args argument, whose value is now passed through as
an argument to the 'run' method of ADAMPlugin.

Added a new example (test) plugin, TakeNPlugin, which shows a simple use of this parameter.
Merge pull request #258 from genomebridge/plugin-args

Adding an 'args' parameter to the plugin framework.
Added AdamContext.referenceLengthFromCigar
Added the TrackedLayout class.
Moving TrackedLayout to the new org.bdgenomics package, fixing method names that have changed.
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.