kshakir 83e207d9dd Added option to exclude intervals during chunk calling. ... Removed job priority as temp space isn't as tight at the moment and planning on changing the priority interface. Updated chunk calling with ebanks: - Using "the bundle" of resources. - Using dbsnp 132 and 1000G indel RODs for both RTC & IR. - Using the default maxIntervalSize in RTC. - Removed use of UG.exactCalculation argument. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5814 348d0f76-0448-11de-a6fe-93d51630548a		2011-05-18 03:48:02 +00:00
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core	Adding another example call set to GATK resource bundle for use in VQSR wiki tutorial	2011-05-05 21:16:33 +00:00
examples	When /etc/mailname is unreadable fall back to the hostname.	2011-04-11 20:22:44 +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	Computes how well a genotype chip covers a reference panel	2011-05-14 15:07:28 +00:00
playground	Added option to exclude intervals during chunk calling.	2011-05-18 03:48:02 +00:00