gatk3的最后一个经典版本3.8

Khalid Shakir fac9932938 Embedding gsalib source and queueJobReport R scripts in the dist and package jars. ... 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().		2011-10-24 15:58:34 -04:00
public	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
settings	Merged bug fix from Stable into Unstable	2011-09-27 14:34:39 -04:00
LICENSE	One last test...	2011-06-28 19:18:17 -04:00
build.xml	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
ivy.xml	Fixed Ant / PluginManager issue where reflections was picking up all class files under current working directory due to "." in jar manifest classpaths.	2011-09-27 14:33:57 -04:00