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Eric Banks 2e36dd9001 Refactoring of CombineGVCFs to make it run a lot faster. 
Creating new VariantContexts each time we broke up a block was very expensive because we break up
blocks so often.  Also, calling into GATKVariantContextUtils.simpleMerge was really hurting performance.

MD5 changes because we no longer propogate any INFO fields (except for END) for reference blocks; the tests
have the now unused BLOCK_SIZE field that now get dropped.
 		2014-02-11 03:18:52 -05:00
..
main/java/org/broadinstitute/sting Refactoring of CombineGVCFs to make it run a lot faster. 2014-02-11 03:18:52 -05:00
test/java/org/broadinstitute/sting Refactoring of CombineGVCFs to make it run a lot faster. 2014-02-11 03:18:52 -05:00