kshakir 787e5d85e9 Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'. ... Added an initial test for genotyping chr20 on ten 1000G bams. Since tribble needs logging support too, for now setting the logging level and appending the console logger to the root logger, not just to "org.broadinstitute.sting". Updated IntervalUtilsUnitTest to output to a temp directory and not the SVN controlled testdata directory. Added refseq tables and dbsnps to validation data in BaseTest. Now waiting up to two minutes for gather parts to propagate over NFS before attempting to merge the files. Setting scatter/gather directories relative to the -run directory instead of the current directory that queue is running. Fixed a bug where escaping test expressions didn't handle delimiters at the beginning or end of the String. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4717 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-22 22:59:42 +00:00
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DispatchJobRunner.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
FunctionEdge.scala	Instead of the pipeline's cleaner only writing BAMs with the target intervals, now pulling the list of contigs from the target intervals and outputing reads in those contigs.	2010-10-22 22:22:30 +00:00
InProcessRunner.scala	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00
JobRunner.scala	Instead of the pipeline's cleaner only writing BAMs with the target intervals, now pulling the list of contigs from the target intervals and outputing reads in those contigs.	2010-10-22 22:22:30 +00:00
LsfJobRunner.scala	Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'.	2010-11-22 22:59:42 +00:00
MappingEdge.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
QEdge.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
QGraph.scala	Excluding the QFunction log files from the set of files to delete on completion.	2010-11-18 20:22:01 +00:00
QGraphSettings.scala	Queue UI Improvements:	2010-10-26 19:49:08 +00:00
QNode.scala	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00
RunnerStatus.scala	QScript authors can now tag functions as intermediate. Functions tagged as intermediate will be skipped unless another function in the graph needs their output.	2010-10-18 22:11:14 +00:00
ShellJobRunner.scala	Instead of the pipeline's cleaner only writing BAMs with the target intervals, now pulling the list of contigs from the target intervals and outputing reads in those contigs.	2010-10-22 22:22:30 +00:00