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12 Commits (71bfb1ee35f6f0ae378d57871fee0c36018c39ce)

Author SHA1 Message Date
depristo b0fc42906e Better DOT support and updated recalibration pipeline 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3811 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-16 20:54:51 +00:00
depristo 6bf5df4eb5 Better merge command 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3797 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-15 17:02:47 +00:00
kshakir 1d399aa2f3 Added a temporary gatkLoggingLevel field to the soon to be obsolete GatkFunction while finishing up the delayed generic gatk walker utility. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3757 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-11 03:27:32 +00:00
kshakir 7be8c35eb2 Workaround for scala trait erasing parameterized types: 
- Requiring explicit @ClassType on parameterized fields in traits.
- Scatter / Gather functions are now abstract classes since @ClassType can't be used on parameterized fields with type parameters.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3726 348d0f76-0448-11de-a6fe-93d51630548a
 2010-07-07 03:15:10 +00:00
kshakir a46e22ed13 Refactored ArgumentDefinition to absorb functionality from ArgumentDefinition and ArgumentTypeDescriptor. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3689 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-30 18:55:57 +00:00
kshakir dce2c17404 Added "-bsubWait" where Queue waits for all the jobs to exit before exiting. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3661 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 19:52:17 +00:00
kshakir c047232b18 Using picard for bam merging. 
Properties now propagate to scatter/gather functions.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3659 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-28 17:59:09 +00:00
kshakir 75c98c42b8 Started path of deprecation of Sting's @Argument by splitting the annotation into @Output and @Input. Anything that's not an @Output should be an @Input. 
Checked in example qscripts that are basically todo integration tests.
Replaced use of queue @Input/@Output with Sting's new @Input/@Output.  This means you'll now have to doc-ument the annotations.
More work on dependency resolution cycles being created in the graph during scatter/gather.
Filtering nulls to avoid NPE exceptions in scala's 'Collection'.hashCode.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3643 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 20:51:13 +00:00
kshakir ce27ed0d60 Added missing @ClassType to memory limits. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3641 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-25 18:56:35 +00:00
kshakir 30cf78fdc0 Refactoring for a first version of scatter gather api with basic shell script implementations. 
Modified build script so that queue is cleaned during "ant clean".



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3611 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-22 18:39:20 +00:00
kshakir c44fd05aa1 Fix for a reflection issue with generic types. 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3565 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-16 15:58:38 +00:00
kshakir 32fc221ffe Replaced pattern matched pipeline spec with annotated objects. 
Old version is no longer available.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3558 348d0f76-0448-11de-a6fe-93d51630548a
 2010-06-15 04:43:46 +00:00