-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)
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)
-- top-level walker type (locus, read etc)
-- parallelism options (nt or nct)
-- annotation type (for Variant Annotations)
-- downsampling settings that override engine defaults
-- reference window size
-- active region settings
-- partitionBy info
-- Added getClazzAnnotations() as hub to retrieve various annotations values and class properties through reflection
-- Added getReadFilters() method to retrieve Read Filter annotations
-- getReadFilters() uses recursion to walk up the inheritance to also capture superclass annotations
-- getClazzAnnotations() stores collected info in doc handler root, which is unit.forTemplate in Doclet
-- Modified FreeMarker template to use the Readfilters info (displayed after arg table, before additional capabilities)
-- Tadaaa :-) #GSATDG-63 resolve
-- Renamed ValidatePileup to CheckPileup since validation is reserved word
-- Renamed AlignmentValidation to CheckAlignment (same as above)
-- Refactored category definitions to use constants defined in HelpConstants
-- Fixed a couple of minor typos and an example error
-- Reorganized the GATKDocs index template to use supercategories
-- Refactored integration tests for renamed walkers (my earlier refactoring had screwed them up or not carried over)
We will use DocumentedGATKFeatures to create categories in our documentation. Eric I guess will be in charge of this. We need to remove walkers and think how to categorize everything.
Tools can be hidden from GATKdocs with the @Hidden annotation
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
GATKDocs looks for a key on gsa4, and updates the forum with new walker if it exists.
More changes were made to the GATKDocs. Works nicely with bootstrap on and offline.
Cleaned up the code as well
Signed-off-by: Mauricio Carneiro <carneiro@broadinstitute.org>
* Did not touch archived walkers... those can be named whatever.
* Kept abstract classes that end in Walker untouched (e.g. LocusWalker, ReadWalker, ...)
* Renamed a few inner classes due to conflict when stripping off Walker from their outer classes: ContigStats, FlagStats and FastaStats.
*New style.css, new template for the walker auto-generated html. Short description is no longer repeated in the long description of the walker.
*Updated DiffObjectsWalker and ContigStatsWalker as "reference" documented walkers.
DiffEngine fixed so that newInstance() would work. Pretty quickly encountered a situation where newInstance() failed. Debug output now written when this occurs in the log.
Logger now used instead of standard out, with INFO the default level.
Required a significant refactoring of the GATKDoclet, which now has a unified place where the ClassDoc, class, annotation, and handler are all stored together.
Index expanded to use summary() annotation field
UserExceptions, ReadFilters, GATK engine all use the system to generate docs
Doclet expanded to handle lots of new cases
Now uses GATKDoc class to organize documentation for arguments.
Arguments now listed by feature (required, optional, hidden, etc) and link to detailed information about the argument in the html
Lots of code moving between Class and ClassDoc objects. Should be refactored into a single static utility class.
Geraldine Van der Auwera
Roger Zurawicki
Mauricio Carneiro
Mark DePristo