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gatk-3.8/scala/src/org/broadinstitute/sting/queue/engine
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kshakir 3e3ff4a9e7 Bam gathering passes on the compression_level and the create_index flag to MergeSamFiles. 
VCF gathering passes on the no_header and sites_only flags to CombineVariants.
Fixed deletion of gathered log files. Although they are intermediate and do not need to be re-run if not present, they should not be deleted.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5508 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-03-25 03:58:38 +00:00
..
gridengine JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706. 2011-03-07 23:52:48 +00:00
lsf Updated LSF libraries to use Pointer instead of Structure.ByReference for struct arrays since the the latter is autoRead() and LSF doesn't always return null for empty arrays. 2011-03-10 22:58:54 +00:00
shell JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706. 2011-03-07 23:52:48 +00:00
CommandLineJobManager.scala JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706. 2011-03-07 23:52:48 +00:00
CommandLineJobRunner.scala JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706. 2011-03-07 23:52:48 +00:00
CommandLinePluginManager.scala JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706. 2011-03-07 23:52:48 +00:00
FunctionEdge.scala JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706. 2011-03-07 23:52:48 +00:00
InProcessJobManager.scala Moved some shutdown logic from the LSF job runner into the QGraph. 2011-01-25 20:28:54 +00:00
InProcessRunner.scala Moved MD5 utils from WalkerTest to BaseTest for use by PipelineTests. 2011-01-25 04:11:49 +00:00
JobManager.scala JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706. 2011-03-07 23:52:48 +00:00
JobRunner.scala JobRunner can be specified on the command line. -bsub is currently short form of -jobRunner Lsf706. 2011-03-07 23:52:48 +00:00
MappingEdge.scala Added pipeline for calling FCP in batches called MultiFullCallingPipeline. 2011-02-15 18:26:14 +00:00
QEdge.scala Added pipeline for calling FCP in batches called MultiFullCallingPipeline. 2011-02-15 18:26:14 +00:00
QGraph.scala Bam gathering passes on the compression_level and the create_index flag to MergeSamFiles. 2011-03-25 03:58:38 +00:00
QGraphSettings.scala Small bug fixes: 2011-03-10 19:54:14 +00:00
QNode.scala Added pipeline for calling FCP in batches called MultiFullCallingPipeline. 2011-02-15 18:26:14 +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