gatk3的最后一个经典版本3.8

kshakir ca5db821ce Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality. ... Queue now submits new LSF jobs only after previous functions have completed successfully. When the Queue process is shutdown (ex: via Control-C) sends a bkill command for any running jobs. Ported commands like creating directories and scatter/gather interval list to scala functions. Updates to LSF status tracking by porting the python to internally generated bash scripts. Temporarily disabled job name submission to LSF. Plus side is that the full command is now available in "bjobs -w". TODO: Put back jobName passing to LSF based on an option? Changed BaseTest to allow scala to access paths to references. Changed the extension generator to default the analysis name to the walker "name". git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4442 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-06 18:29:56 +00:00
R	Better reporting -- figured out how to drop unused levels in subset	2010-10-06 14:31:51 +00:00
archive	Cleaning up playground utils and tests	2010-08-27 01:25:47 +00:00
c	Reduce file handle usage.	2010-01-05 18:03:01 +00:00
doc	removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also	2010-08-19 00:42:37 +00:00
java	Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.	2010-10-06 18:29:56 +00:00
matlab	Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function	2009-11-30 20:02:25 +00:00
packages	/broad/1KG doesn't exist	2010-10-06 12:54:38 +00:00
perl	update the example: /broad/1KG doesn't exist anymore	2010-10-05 13:50:24 +00:00
python	Shorter outputs, new summary mode	2010-10-06 14:34:50 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.	2010-10-06 18:29:56 +00:00
settings	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
shell	minor improvements to queue status	2010-10-06 14:34:35 +00:00
testdata	Fixes for example bam files	2010-10-05 18:43:02 +00:00
LICENSE	Adding a license to the root directory in case BOSC checks for one. Has the	2010-04-20 16:04:29 +00:00
build.xml	Fixed re-builds of queue so that previously compiled classes are included. Fixes redundant case of "ant queue test" vs. "ant test".	2010-10-04 21:12:07 +00:00
ivy.xml	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +00:00