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
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alignment	all fixed..thanks Matt!	2010-09-10 06:18:59 +00:00
commandline	Final step in error refactoring. GATK exception is now ReviewedStingException, indicating that this exception is really what one wants. Only use this exception when you have thought about StingException vs. UserException and made a real decision.	2010-09-12 15:07:38 +00:00
datasources/pipeline	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +00:00
gatk	Added command line argument for the max value of the allele count prior in VariantRecalibrator (--max_ac_prior). Default value increased to 0.99 from 0.95.	2010-10-06 14:00:53 +00:00
oneoffprojects/walkers	The tribble indexes are now updated with correct sequence lengths for each contig they have in their sequence dictionary. Also clean-up in the RMD track builder.	2010-09-21 18:21:22 +00:00
playground/gatk/walkers	Recent changes to the build system make the build system complain loudly about	2010-09-24 22:09:12 +00:00
utils	At some time in the recent past, we lost our ability to process the '-L all'	2010-09-30 15:58:43 +00:00
BaseTest.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
WalkerTest.java	Added a back door so that integration tests can reset the sequence dictionary	2010-09-14 18:58:08 +00:00