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.
Modifying conversion code to resolve #112.
Merge pull request #260 from fnothaft/sanity-check-flags

Modifying conversion code to resolve #112.
Adding RichADAMRecord.referenceLengthFromCigar

The new referenceLengthFromCigar method (and its associated ADAMRecord method, 'referenceLength')
is an implementation of a method which counts the length of an aligned read against the reference
sequence. This is useful because rec.start + rec.referenceLength is a logical "end" coordinate
to be used for testing overlap of an ADAMRecord against a reference range.
Merge pull request #263 from genomebridge/tdanford/referenceLengthFromCigar

Added AdamContext.referenceLengthFromCigar