Adds toString method for sequence dictionary. Also cleans up printing to stdout during unit tests.
Merge pull request #257 from fnothaft/fix-seqdict-printout

Adds toString method for sequence dictionary.
Updated Spark version to 1.0.0

Also adding the fastutil dependency back in. Spark 0.9 had included the dependency on
fastutil, which we also depended on! But Spark 1.0 apparently removes that dependency.
So this commit adds that back in, for our own use.
Updating all instances of Seq[_] to Iterable[_] in RDD.groupBy()

Apparently, the signature for the RDD.groupBy method has changed (in 1.0) to return an Iterable
rather than a Seq.  This commit includes all the changes taht are needed to account for this change
downstream in our code, mostly updating types to Iterable and inserting a few calls to toSeq in cases
where that's not sufficient.
Updated kryo.referenceTracking parameter, fixed test values.

As suggested by Matt and Frank, updated two things:
1. the spark.kryo.referenceTracking value, set to 'true', which fixes a StackOverflowError, and
2. updated the target (test) values for the IndelRealignmentTargetSuite tests, which Frank says are apparently
   going to change soon anyway.
Upgrade to Avro version 1.7.6

See the thread here: https://issues.apache.org/jira/browse/SPARK-1851
Removed an unused import in AvailableComparisons
Merge pull request #256 from genomebridge/spark-1.0

Upgrading to Spark 1.0
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