kshakir 8ba3a5a43f Command lines for locally run Queue jobs no longer have to be escaped differently than bsub'ed jobs. ... GSA-410 Local job runs now can run command lines longer than than 4096 on our linux machines. When determining if the help text and Queue extensions need to be rebuilt, use the .class files not the .java so that GATK oneoffs are picked up correctly. Added the most basic of all example QScripts for debugging, Hello World. Minor updates to copy/pasted LSF code to reduce ant javadoc warnings by a third. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4970 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-10 21:07:29 +00:00
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config	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
src	Command lines for locally run Queue jobs no longer have to be escaped differently than bsub'ed jobs.	2011-01-10 21:07:29 +00:00
test	Implemented a new argument (-DQS --defaultQualityScore) that allows GATK to deal with BAM files missing quality scores. If a value is specified, all reads are filled with the default quality score. Appropriate exception is thrown if -DQS is not provided and BAM file doesn't have quality scores for every base.	2011-01-05 22:25:08 +00:00