* Added support for a protected directory whose contents are only made public in binary form
* Simplified and reorganized build.xml to improve readability and maintainability
* build.xml now autodetects most build properties:
-Includes private/protected if they exist
-No more STING_BUILD_TYPE or specialized targets for public-only, etc.
* Build targets have changed! There are now two main build options:
"ant" build everything (GATK and Queue)
"ant gatk" build just the GATK
It was too hard to build everything before -- now it is the default.
* To run tests with debugging, use -Dtest.debug=true -Dtest.debug.port=XXXX on the command line.
Much better than the old comment/uncomment method!
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().
David Roazen
Khalid Shakir