* Moved GATKArgumentCollection into gatk.arguments folder to clean up the main folder, also added some associated argument classes (most of the changes).
* Added code the argument parsing system for default enums, we needed this so we could preserve the current unsafe flag, and at the same time allow finer grained control of unsafe operations. You can now specify:
"-U" (for all unsafe operations), "-U ALLOW_UNINDEXED_BAM" (only allow unindexed BAMs), "-U NO_READ_ORDER_VERIFICATION", etc.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2586 348d0f76-0448-11de-a6fe-93d51630548a
depristo
hanna
ebanks
asivache
aaron