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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%
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hanna a8caa20378 Previously the hierarchical microscheduler defensively coded around and reported exceptions of 
the walker itself, but didn't do a great job of catching framework exceptions.  This became extremely
unfortunate in the case where walkers caused exceptions that manifested themselves in the framework,
such as when the walker opens more files than file handles are available.

Reworked the exception handling so that framework errors are treated like walker errors and the resulting
exception bubbles out of the walker.  Stack traces for threaded walkers are still convoluted and nasty.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3794 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-07-14 20:34:43 +00:00
R Can run R scripts on the command line 2010-07-09 00:13:18 +00:00
archive Deleting/archiving as instructed 2010-07-13 15:23:50 +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 Previously the hierarchical microscheduler defensively coded around and reported exceptions of 2010-07-14 20:34:43 +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 Update to the latest rev of the picard sharding patch. Includes updates reflecting 2010-06-06 20:33:21 +00:00
perl 1. Updated tests and added integration test for liftover code. 2010-07-12 17:58:18 +00:00
python Restore "type" annotation (but not genomechange or cDNA change, which are already encoded in the VCF) 2010-07-13 17:33:15 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +00:00
scala Intermediate commit of scatter/gather recalibation pipeline 2010-07-13 22:46:08 +00:00
settings Rev Picard with new IndexedFastaSequenceFile patch. 2010-07-01 03:05:43 +00:00
shell a) Add input argument (-ncrate) to BeagleOutputToVCFWalker. If the genotype posterior error probability is higher than this threshold, we declare No-call at this genotype. 2010-07-06 18:33:28 +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 adding Ivy lines for findbug, and adding a build task (to run it locally you need to have installation of findbug). I'll put more information on the wiki when it's up and running. 2010-07-08 19:10:19 +00:00
ivy.xml adding Ivy lines for findbug, and adding a build task (to run it locally you need to have installation of findbug). I'll put more information on the wiki when it's up and running. 2010-07-08 19:10:19 +00:00