--Refactored listAnnotations basic method out of VA into HelpUtils
--HelpUtils.listAnnotations() is now called by both VA and the new ListAnnotations utility (lives in sting.tools)
--This way we keep the VA --list option but we also offer a way to list annotations without a full valid VA command-line, which was a pain users continually complained about
--We could get rid of the VA --list option altogether ...?
-- 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)
-- Sorted out contents of BAM Processing vs. Diagnostics & QC Tools
-- Moved two validation-related walkers from Diagnostics & QC to Validation Utilities
-- Reworded some category names and descriptions to be more explicit and user-friendly
-Moved some of the more specialized / complex VariantContext and VCF utility
methods back to the GATK.
-Due to this re-shuffling, was able to return things like the Pair class back
to the GATK as well.
This will prevent bugs from occurring when Vanilla make changes to the API
as described here: http://vanillaforums.com/blog/api#configuration
Based on the bug that broke the website Guide section on 9/6/12,
the GATKDocs posting system will probably break in the next release if
this is not applied as a bug fix.
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.
-- Sorting of ArgumentSources now done in GATKDoclet, not in the ParsingEngine, as the system depends on the LinkedTreeMap
-- Fixed broken exception throwing in the case where a file's type could not be determined
-- ArgumentSources are now sorted by case insensitive names, so arguments are shown in alphabetical order (Ryan)
-- @Advanced annotation can be used to indicate that an argument is an advanced option and should be visually deemphasized in the GATKs. There's now an advanced section. Mauricio or Ryan -- could you figure out how to make this section less prominent in the style.css?
-- Allowed values for RodBinding<T> are displayed in the GATKDocs
-- Longest name up to 30 characters is chosen for main argument list (suggested by Ryan/Mauricio)
-- Features are listed in alphabetical order
-- Moved useful getParameterizedType() function to JVMUtils
-- Tests of these features in the Documentation Test
-- Now supports a static list of root classes / interfaces that should receive docs. A complementary approach to documenting features to the DocumentedGATKFeature annotation
-- Tribble codecs are now documented!
-- No longer displayed sub and super classes
-- DocString function for types that create default outputs "stdout"
-- RodBinding now creates a makeUnbound default value automatically for you if your RodBinding isn't required
-- Removed warning about sparse help from TextFormattingUtils
*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.
Geraldine Van der Auwera
David Roazen
Mauricio Carneiro
Eric Banks
Randal Moore
kshakir
Geraldine Van der Auwera
Mark DePristo
Roger Zurawicki