chartl 07d381ec51 BatchMerge now uses the correct UG settings, recently added by Eric ... ExpandIntervals now checks that identical intervals are not created by (un)fortunately-spaced targets VCFExtractIntervals no longer creates duplicate intervals in the case where a VCF has multiple entries at the same site git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5294 348d0f76-0448-11de-a6fe-93d51630548a		2011-02-23 18:46:15 +00:00
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core	Few organizational changes, queue output is now categorized and hidden. Also changed NA12878.Wex to dbsnp 129.	2011-02-22 22:49:38 +00:00
examples	Moved the maximum number of intervals check from FCP to the Queue core so that scatter gather will no longer blow up if you specify a scatter count that is too high.	2011-01-28 23:33:58 +00:00
lib	Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires.	2010-12-15 03:33:36 +00:00
oneoffs	now only accepts intervals files if the user specifically requests to report bams at interval only.	2011-02-23 16:49:58 +00:00
playground	BatchMerge now uses the correct UG settings, recently added by Eric	2011-02-23 18:46:15 +00:00