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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carneiro	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
chartl	Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.	2011-01-07 22:03:36 +00:00
depristo	phasing per sample. tmp checkin	2010-12-22 20:14:06 +00:00
examples	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
hanna	Trying out Queue for the first time.	2010-11-18 18:29:12 +00:00
kshakir	Checking in scripts used for testing the linear index MAX_FEATURES_PER_BIN.	2010-12-20 21:25:36 +00:00
lib	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
rpoplin	In the Methods development pipeline the call confidence threshold must be lowered from the default value for lowpass calling. What a bone-headed mistake!	2011-01-05 20:30:55 +00:00
fullCallingPipeline.q	Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.	2011-01-07 22:03:36 +00:00
recalibrate.scala	- After removing special code for intervals, instead of being of type File they are generated as List[File]. Changed previous checkin that was appending to this list and instead assigning a singleton list.	2010-10-21 06:37:28 +00:00