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.
This is very useful and easy. After running any test (for example ant integrationtest) and seeing failures, you can rerun ONLY THE TESTS THAT FAILED by using one of the following commands:
ant failed-integration
ant failed-pipeline
ant failed-test
ant failed-performance
obviously matching whatever tests you were running and got failures on.
This should run only the failed tests, and you can keep using this command until you have fixed everything.
(Thanks to David Roazen for major help with ANT)
The NullPointerException we were seeing when trying to run with contracts enabled was being caused
by an outdated version of the asm library.
To run tests without contracts and disable their compilation, pass in "-Duse.contracts=false" to ant.
Also did some minor unrelated cleanup in build.xml
describe" as an absolute version number (if the repository has at least one
tag), using the raw SHA-1 hash value as a fallback version number in the case
where there are no tags.
Temporarily disabled contracts in integrationtests until we can find the cause
of the new error that's cropping up for Ryan.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5967 348d0f76-0448-11de-a6fe-93d51630548a
Current tribble-129M.jar in SVN does not work with current version of GATK code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5897 348d0f76-0448-11de-a6fe-93d51630548a
only download that test configuration when running unit/integration tests.
This means that the build will (hopefully) never break because it can't
fetch a file that isn't required for the GATK to run.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5775 348d0f76-0448-11de-a6fe-93d51630548a
Also added the old model of indel calling to the FCP.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5749 348d0f76-0448-11de-a6fe-93d51630548a
Using the VCFWriterATD isCompressed to check if the VCF index will be auto generated.
Tracking BAM and Tribble indexes as @Inputs and @Outputs in generated QFunctions.
Updates to the BamGatherFunction to disable the index during merge when disable_bam_indexing = true.
Made a shortcut for live-running pipelinetest, pipelinetestrun.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5606 348d0f76-0448-11de-a6fe-93d51630548a
extracted from source files that have been modified since the help resource
file was last generated. This significantly speeds up builds where only a few
source files have been modified, at the expense of making clean builds take
slightly longer. Here's some performance data gathered by testing the old and
new versions of extracthelp in isolation and averaging across 10 runs:
old extracthelp, 1 modified source file: 20.1 seconds
new extracthelp, 1 modified source file: 7.2 seconds <-- woohoo! :)
old extracthelp, clean build: 17.8 seconds
new extracthelp, clean build: 20.5 seconds
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5590 348d0f76-0448-11de-a6fe-93d51630548a
Custom gatherer prints out the class name in the logs.
Try to retrieve mail domain from /etc/mailname before falling back to the hostname.
Building oneoff jars during ant oneoffs.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5540 348d0f76-0448-11de-a6fe-93d51630548a
Added a property to allow generating Queue extensions around an external version of the GATK.
Updated argument order in -help.
Restored the ability to use QScript trait imported annotations in constructors.
Removing line feeds from email password files.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5416 348d0f76-0448-11de-a6fe-93d51630548a
Added an empty wrapper for a GridEngine job runner which is only activated when SGE_ROOT is detected.
Refactored a bit more common code into CommandLineJobRunner / JobRunner / FunctionEdge.
Status for analyisNames now includes the number of functions in state.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5399 348d0f76-0448-11de-a6fe-93d51630548a
Mark DePristo
Khalid Shakir
Mauricio Carneiro
David Roazen
Matt Hanna
ebanks
depristo
hanna
kshakir
droazen
kcibul