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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R	Something changed with the ggtitle syntax in the latest version of ggplot2.	2013-08-14 14:40:03 -04:00
c	At chartl's request, add the bwa aln -N and bwa aln -m parameters to the bindings.	2012-01-17 14:47:53 -05:00
chainFiles	…
doc	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
java	Assorted fixes and improvements to gatkdocs	2014-01-13 17:46:22 -05:00
keys	Public-key authorization scheme to restrict use of NO_ET	2012-03-06 00:09:43 -05:00
packages	ValidatingPileup was renamed to CheckPileup	2013-02-15 11:56:19 -05:00
perl	Fixing the liftover script to not require strict VCF header validation.	2013-11-07 09:02:17 -05:00
scala	Merge remote-tracking branch 'origin/master' into mf_new_RBP	2013-12-19 10:42:20 -05:00
testdata	Walker to create a fastq file from an interval list	2013-06-29 11:24:16 -04:00