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.
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by an outdated version of the asm library.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
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
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.
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though sonatype is back up). This will tide us over until I figure out how
to add caliper to test configuration, so that it's only swapped in when we
actually run our unit / performance tests.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5770 348d0f76-0448-11de-a6fe-93d51630548a
but I'm still not sure that GC is a good long-term solution.
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- bsub command line is no longer fully printed out.
- extraBsubArgs hack is now a callback function updateJobRun.
Updated FullCallingPipelineTest to reflect latest changes to fullCallingPipeline.q.
Added a pipeline that tests the UGv2 runtimes at different bam counts and memory limits.
Updated VE packages that live in oneoffs to compile to oneoffs.
Added a hack to replace the deprecated symbol environ in Mac OS X 10.5+ which is needed by LSF7 on Mac.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4816 348d0f76-0448-11de-a6fe-93d51630548a
Shell invoking scripts so that even really long shell scripts make it through LSF.
Using the truncated (up to 1000 characters) of the command line for the job name for use with bjobs.
Switched the default from re-running everything to re-running only files that need to be regenerated. --skip_up_to_date replaced with --start_clean for those who want to regenerate everything.
Updated logging to let users know when the scatter gather generator is running, which still takes a while but is orders of magnatudes faster for large lists of functions. (40s for a 100 function graph exploding to a 2500 function graph)
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removed the auto-deletion of the reflections jar, and removed the very old OmniPlan document we had checked-in.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4056 348d0f76-0448-11de-a6fe-93d51630548a
Changes to StingUtils command line for use in Queue, replacing Queue's use of property files.
Updates to walkers used in existing QScripts to add @Input/@Output.
RMD used in @Required/@Allows now has a new default equal to "any" type.
New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions.
Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.)
Removed dependency on BroadCore by porting LSF job submitter to scala.
Ivy now pulls down module dependencies from maven.
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features in that contig. Thanks to Mark for finding this. I'm not rev'ing the index version (which would cause all indexes to be rebuilt), since this seems like a pretty rare edge case.
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- makes writing to disk optional for indexes using the indexCreator classes (allow the user to specify the index file, if null don't write it)
- removed some system.out debugging code
- fixed version checking in interval tree
- made indexes store and return a LinkedHashSet for sequence names (to ensure they've preserved the ordering in the file)
- index creators now read the file before creating the index
- changed the Index.write() method to take a LEDataStream instead of a file
- removed the sequence dictionary code on the header
- added utils for getting LEDataStreams
- added a base Tribble exception
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3857 348d0f76-0448-11de-a6fe-93d51630548a
Mark DePristo
David Roazen
Matt Hanna
Khalid Shakir
droazen
hanna
depristo
kshakir
aaron