Moved gsalib and queueJobReport.R to embeddable namespaced locations.
Updated packager dependencies/dir to add an @includes which filters the embedded fileset.
RScriptExecutor can now JIT compiles the gsalib.
RScriptExecutor uses ProcessController and sends the Rscript output to java's stdout when run under -l DEBUG.
Refactored ProcessController and IOUtils from Queue to Sting Utils.
Added more unit tests to ProcessController along with a utility class to hard stop OutputStreams at a specified byte count.
Replaced uses of some IOUtils with Apache Commons IO.
ShellJobRunner refactored to use direct ProcessController and now kills jobs on shutdown.
Better QGraph responsiveness on shutdown by using Object.wait() instead of Thread.sleep().
Moved the validation of the GATKSamRecord to the MalformedReadFilter with the intent to make the read filter the ultimate validation location for sam records. This way we can opt to filter out malformed reads if we know what we are doing or blow up otherwise.
This commit contains:
- IntronLossGenotyper is brought into its current incarnation
- A couple of simple new filters (ReadName is super useful for debugging, MateUnmapped is useful for selecting out reads that may have a relevant unaligned mate)
- RFA now matches my current local repository. It's in flux since I'm transitioning to the new traversal type.
+ the triggering read stash pilot required me to change the scope of some of the variables in the ReadClipping code, private -> protected. Those are all the changes there.
- MendelianViolation restored to its former glory (and an annotator module that uses the likelihood calculation has been added)
+ use this rather than a hard GQ threshold if you're doing MV analyses.
- Some miscellaneous QScripts
-- all of the methods in the class must be synchronized or the internal state can be inconsistent with the contract invariant when entering the class in a non-synchronized method, even when that method doesn't care about the object's internal state
We can't have a public test that depends on both public and private
code/data -- the new release system needs to do public-only tests,
and will catch this sort of thing.
-Added targets to run unit and integration tests on the fully-packaged GATK jar,
and pipeline tests on the fully-packaged Queue jar. Once enabled in Bamboo,
these will provide greatly-enhanced protection against breakage in the binary
release.
-Unconditionally include all of the subset of org.broadinstitute.sting
included in the intermediate jars GenomeAnalysisTK.jar, StingUtils.jar,
etc. in the final, fully-packaged jar. This:
* is necessary to get tests to run on the fully-packaged jar
* decreases the chances of a class that is a runtime-only
dependency getting left out of the binary release
* only slightly increases the size of the binary release
(before: 9352465 bytes, after: 10985482 bytes)
The public integration test VariantContextIntegrationTest was dependent on the
private walker TestVariantContextWalker. Moved this walker to public/java/test
(NOT public/java/src, since this walker is only used by the test suite) to avoid
errors during public-only tests.
Ryan Poplin
David Roazen
Guillermo del Angel
Khalid Shakir
Mark DePristo
Mauricio Carneiro
Christopher Hartl
Eric Banks
Menachem Fromer