07b369ca7e
This is an intermediate commit so that there is a record of these changes in our commit history. Next step is to isolate the test classes as well, and then move the entire package to the Picard repository and replace it with a jar in our repo. -Removed all dependencies on org.broadinstitute.sting (still need to do the test classes, though) -Had to split some of the utility classes into "GATK-specific" vs generic methods (eg., GATKVCFUtils vs. VCFUtils) -Placement of some methods and choice of exception classes to replace the StingExceptions and UserExceptions may need to be tweaked until everyone is happy, but this can be done after the move. |
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