New CLP to update the sequence dictionary for one with VCF with that from another.
Moved Yossi's SAMSequenceDictionaryExtractor over to htsjdk from picard
Merged same into UpdateVcfSequenceDictionary code.
Merge pull request #71 from broadinstitute/gg_UpdateVcfDictionary

A new CLP to update the sequence dictionary of a VCF from another file (SAM, BAM, VCF, dictionary, interval_list, fasta, etc).