- By porting from jython to java now accessible to Queue via automatic extension generation.
- Better handling for problematic sample names by using PicardAggregationUtils.
GATKReportTable looks up keys using arrays instead of dot-separated strings, which is useful when a sample has a period in the name.
CombineVariants has option to suppress the header with the command line, which is now invoked during VCF gathering.
Added SelectHeaders walker for filtering headers for dbGAP submission.
Generated command line for read filters now correctly prefixes the argument name as --read_filter instead of -read_filter.
Latest WholeGenomePipeline.
Other minor cleanup to utility methods.
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().
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.
Mauricio Carneiro
Khalid Shakir
David Roazen
Mark DePristo