Geraldine Van der Auwera 8fcad6680b Assorted fixes and improvements to gatkdocs ... -Added docs for ERC mode in HC -Move RecalibrationPerformance walker since to private since it is experimental and unsupported -Updated VR docs and restored percentBad/numBad (but @Hidden) to enable deprecation alert if users try to use them -Improved error msg for conflict between per-interval aggregation and -nt -Minor clean up in exception docs -Added Toy Walkers category for devs and dev supercat (to build out docs for developers) -Added more detailed info to GenotypeConcordance doc based on Chris forum post -Added system to include min/max argument values in gatkdocs (build gatkdocs with 'ant gatkdocs' to test it, see engine and DoC args for in situ examples) -Added tentative min/max argument annotations to DepthOfCoverage and CommandLineGATK arguments (and improved docs while at it) -Added gotoDev annotation to GATKDocumentedFeature to track who is the go-to person in GSA for questions & issues about specific walkers/tools (now discreetly indicated in each gatkdoc)		2014-01-13 17:46:22 -05:00
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java	Assorted fixes and improvements to gatkdocs	2014-01-13 17:46:22 -05:00
scala/test/org/broadinstitute/sting/queue/pipeline/examples	Fix improper dependencies in QScripts used by pipeline tests, and attempt to fix the flawed MisencodedBaseQualityUnitTest	2013-02-27 04:45:53 -05:00