chartl eb200e4cce Hrumph. Don't just add pointers to the same objects, actually clone the underlying arrays. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3379 348d0f76-0448-11de-a6fe-93d51630548a		2010-05-18 17:13:44 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src/org/broadinstitute/sting	Hrumph. Don't just add pointers to the same objects, actually clone the underlying arrays.	2010-05-18 17:13:44 +00:00
test/org/broadinstitute/sting	Major refactoring of Depth of Coverage to allow for more extensible partitions of data (now can do read group, sample, and library; in any combination; adding more is fairly easy). Changed the by-gene code to use clones of stats objects, rather than munging the interval DoCs. (Fix for Avinash. Who, hilariously, thinks my name is Carl.) Added sorting methods to ensure static ordering of header and body fields.	2010-05-18 16:58:13 +00:00