Fixed bug in setSequenceDictionary where updated contigs not being set properly

When using setSamSequenceDictionary, there were some problems:
1) The new updated VCFContigHeaderLines were being added to contigMetaData, but the overall mMetaData was not being cleared of the old contig header lines and then all being readded.
2) The assembly (i.e. "b37") was not being added properly to the contig header line and when written, it was written in the wrong order.
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