kshakir fd5970fdd4 At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them. ... No longer generating deprecated GATK arguments on the Queue extensions. Emitting deprecation warnings to Queue compile to help debugging issues. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4195 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-02 21:30:48 +00:00
..
engine	Back to using the LSF job name during dry runs since when the real job ids weren't available '-w(null)' wasn't too informative.	2010-08-25 15:18:02 +00:00
extensions	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.	2010-09-02 21:30:48 +00:00
function	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.	2010-09-02 21:30:48 +00:00
util	Command-line argument tagging is in, and the ROD system is hacked slightly to support the new syntax	2010-08-25 03:47:57 +00:00
QCommandLine.scala	Cleaning up Queue debugging output.	2010-08-13 15:54:08 +00:00
QException.scala	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.	2010-06-25 20:51:13 +00:00
QScript.scala	Changed logging level to default at INFO instead of WARN.	2010-08-09 16:42:48 +00:00
QScriptManager.scala	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.	2010-09-02 21:30:48 +00:00
QSettings.scala	Created a new playground script for cleaning bams in Firehose.	2010-08-13 23:52:24 +00:00