gatk-3.8

gatk3的最后一个经典版本3.8

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chartl 9d2a485532 Update to AminoAcidTransition eval module git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3783 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-13 17:12:03 +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	Update to AminoAcidTransition eval module	2010-07-13 17:12:03 +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	Altering the formatting of the annotation to work better with VariantEval's AminoAcidTransition	2010-07-13 16:31:14 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala	Added a temporary gatkLoggingLevel field to the soon to be obsolete GatkFunction while finishing up the delayed generic gatk walker utility.	2010-07-11 03:27:32 +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