Ryan Poplin 487fb2afb4 Bug fix for the case of overlapping assembled and partially-assembled events created by the HC. Unfortunately the symbolic allele can't be combined with the indel allele because the reference basis will change.		2013-01-09 15:30:46 -05:00
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config	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
src	Bug fix for the case of overlapping assembled and partially-assembled events created by the HC. Unfortunately the symbolic allele can't be combined with the indel allele because the reference basis will change.	2013-01-09 15:30:46 -05:00
test	Move some classes back to public because they are used in the engine. Move some test classes to protected. We should have no more public->protected dependancies now	2013-01-09 11:06:10 -05:00