Remove extraneous initLogging() calls
Upgrade to Spark 0.9 and Scala 2.10
Step 1 towards fixing indel realignment.
Fix for serialization issues.
Fixes a left normalization issue.
Refactoring indel target generation code to reduce shuffle traffic.
Temporarily removing serialization buffer setting.
Twist to rod functions.
Added switches to spark context creation code to allow buffer size increase and increased logging for profiling.
Refactored SequenceDictionary aggregation to eliminate replication between RDD extensions.
Merge branch 'context-debug' into indel-realigner-cleanup

Conflicts:
	adam-core/src/main/scala/edu/berkeley/cs/amplab/adam/serialization/AdamKryoProperties.scala
Merge branch 'sequence-dictionary-rdd-funcs' into indel-realigner-cleanup
Upgrading to use new sequence dictionary function.
Making Sequence Dictionary immutable.
Merge branch 'sequence-dictionary-rdd-funcs' into indel-realigner-cleanup
Refactoring aggregate into map reduce.
Merge branch 'sequence-dictionary-rdd-funcs' into indel-realigner-cleanup
Further revisions to dictionary collection.
Merge branch 'sequence-dictionary-rdd-funcs' into indel-realigner-cleanup
Updated to reduce GC overhead.