ebanks dd1d9cd76f Forgot to deprecate the old args ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6009 348d0f76-0448-11de-a6fe-93d51630548a		2011-06-16 17:54:44 +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	Forgot to deprecate the old args	2011-06-16 17:54:44 +00:00
test	[Foiled yet again when trying to do this in git] Slight modifications in the argument structure for the IndelRealigner. Instead of boolean flags -knownsOnly and -doNotUseSW, we now have an enum --consensusDeterminationModel which lets you specify knowns only, also use indels in reads, or also use SW. Please note that the default behavior of IR has not changed at all (and won't for a few more days) - that'll be done in GIT (fingers crossed).	2011-06-16 17:35:37 +00:00