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
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R	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
c	Reinitialize random seed in the bwa bindings from the fixed seed stored in the	2011-07-22 13:41:53 -04:00
chainFiles	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
doc	Reorganized the codebase beneath top-level public and private directories,	2011-06-28 06:55:19 -04:00
java	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
packages	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
perl	Update to the bindings for liftOverVCF.pl (to -V from -B)	2011-09-15 15:33:09 -04:00
scala	Embedding gsalib source and queueJobReport R scripts in the dist and package jars.	2011-10-24 15:58:34 -04:00
testdata	Oops, forgot the PED test file	2011-10-05 21:09:08 -07:00