Geraldine Van der Auwera f972963918 Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs) ... GATK-73 updated docs for bqsr args GATK-9 differentiate CountRODs from CountRODsByRef GATK-76 generate GATKDoc for CatVariants GATK-4 made resource arg required GATK-10 added -o, some docs to CountMales; some docs to CountLoci GATK-11 fixed by MC's -o change; straightened out the docs. GATK-77 fixed references to wiki GATK-76 Added Ami's doc block GATK-14 Added note that these annotations can only be used with VariantAnnotator GATK-15 specified required=false for two arguments GATK-23 Added documentation block GATK-33 Added documentation GATK-34 Added documentation GATK-32 Corrected arg name and docstring in DiffObjects GATK-32 Added note to DO doc about reference (required but unused) GATK-29 Added doc block to CountIntervals GATK-31 Added @Output PrintStream to enable -o GATK-35 Touched up docs GATK-36 Touched up docs, specified verbosity is optional GATK-60 Corrected GContent annot module location in gatkdocs GATK-68 touched up docs and arg docstrings GATK-16 Added note of caution about calling RODRequiringAnnotations as a group GATK-61 Added run requirements (num samples, min genotype quality) Tweaked template and generic doc block formatting (h2 to h3 titles) GATK-62 Added a caveat to HR annot Made experimental annotation hidden GATK-75 Added setup info regarding BWA GATK-22 Clarified some argument requirements GATK-48 Clarified -G doc comments GATK-67 Added arg requirement GATK-58 Added annotation and usage docs GSATDG-96 Corrected doc Updated MD5 for DiffObjectsIntegrationTests (only change is link in table title)		2013-03-12 10:57:14 -04:00
..
engine	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
extensions	Fixed issues raised by Appistry QA (mostly small fixes, corrections & clarifications to GATKDocs)	2013-03-12 10:57:14 -04:00
function	Added a QFunction.jobLocalDir for optionally tracking a node local directory that may have faster intermediate storage, with SGF ensuring that if the directory happens to be on the same machine that it get's a clone specific sub-directory to avoid collisions.	2013-01-25 14:28:04 -05:00
library	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
util	Re-committing the following changes from Dec 18:	2013-01-16 12:43:15 -05:00
QCommandLine.scala	Message "script failed" moved to the correct place in the code	2013-02-04 15:37:23 -05:00
QCommandPlugin.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QException.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QScript.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QScriptManager.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00
QSettings.scala	Updating licenses for all scala files	2013-01-10 17:46:10 -05:00