chartl 3e75431bc8 Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4842 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-15 03:33:36 +00:00
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engine	Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects:	2010-12-10 04:36:06 +00:00
extensions	Tightening of the batch merging pipeline. Optimized to run on hour queue, so please: if you run this, crush 'hour' with it. Testing is forthcoming, but it merged 700 samples overnight.	2010-12-08 14:36:23 +00:00
function	Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects:	2010-12-10 04:36:06 +00:00
library	Thanks to mark: VCFInfoToTable removed in favor of a more flexible walker. Slight change to the argument structure of the walker to make it play more nicely with Queue: the field list parsing is pushed into the command line system (e.g. the variable is exposed as a List<String> and not a String, so Queue doesn't have to join a list into a string only to have it broken out again. This also allows the user to specify -F field1 -F field2 -F field3 if he/she so desires.	2010-12-15 03:33:36 +00:00
pipeline	Updates and bug fixes to private mutations qscript and pipeline libraries. Hand filter strings are now not busted (boo to having to escape quotes); convenience method added to VariantCalling to propagate standard trait data to a given GATK command line -- should be made more scala-esque in the future.	2010-12-13 04:55:13 +00:00
util	Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects:	2010-12-10 04:36:06 +00:00
QCommandLine.scala	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +00:00
QException.scala	Fix for Queue	2010-09-12 15:18:08 +00:00
QScript.scala	java changes:	2010-12-12 05:10:45 +00:00
QScriptManager.scala	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +00:00
QSettings.scala	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +00:00