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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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kshakir 4f51a02dea Changed logging level to default at INFO instead of WARN. 
Changes to StingUtils command line for use in Queue, replacing Queue's use of property files.
Updates to walkers used in existing QScripts to add @Input/@Output.
RMD used in @Required/@Allows now has a new default equal to "any" type.
New QueueGATKExtensions.jar generator for auto wrapping walkers as Queue CommandLineFunctions.
Added hooks to modify the functions that perform the Scattering and Gathering (setting their jar files, other arguments, etc.)
Removed dependency on BroadCore by porting LSF job submitter to scala.
Ivy now pulls down module dependencies from maven.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3984 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-08-09 16:42:48 +00:00
R Publication tranches report is now the default output 2010-08-07 13:58:59 +00:00
archive Archiving 2010-07-27 02:47:18 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java Changed logging level to default at INFO instead of WARN. 2010-08-09 16:42:48 +00:00
matlab Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function 2009-11-30 20:02:25 +00:00
packages Updated resources package descriptor with dbsnp 129 for b37. 2010-08-03 02:42:48 +00:00
perl 1. Updated tests and added integration test for liftover code. 2010-07-12 17:58:18 +00:00
python now support -o output option, useful for pipelines 2010-08-06 14:57:04 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +00:00
scala Changed logging level to default at INFO instead of WARN. 2010-08-09 16:42:48 +00:00
settings Changed logging level to default at INFO instead of WARN. 2010-08-09 16:42:48 +00:00
shell Useful script to see the status of gsa computing resources. Crontab'd and will be arriving as email at 8 am 2010-08-07 12:36:28 +00:00
testdata and add changes to the vcf used in testing 2010-06-25 02:56:02 +00:00
LICENSE Adding a license to the root directory in case BOSC checks for one. Has the 2010-04-20 16:04:29 +00:00
build.xml Changed logging level to default at INFO instead of WARN. 2010-08-09 16:42:48 +00:00
ivy.xml Changed logging level to default at INFO instead of WARN. 2010-08-09 16:42:48 +00:00