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David Roazen a536e1da84 Move some VCF/VariantContext methods back to the GATK based on feedback 
-Moved some of the more specialized / complex VariantContext and VCF utility
 methods back to the GATK.

-Due to this re-shuffling, was able to return things like the Pair class back
 to the GATK as well.
 		2013-01-29 16:56:55 -05:00
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sting Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00
variant Move some VCF/VariantContext methods back to the GATK based on feedback 2013-01-29 16:56:55 -05:00