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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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hanna 5f1b67c1de Coping out and forcing the entire GATK (and associated JVM) to use US English 
locale.  Method to force JVM into proper locale exists in CommandLineProgram
and is disabled by default, but implementers of CommandLineProgram can opt in
to the forced US locale by calling a static method.

Question for the VCF developers: I removed the code to explicitly output doubles
in US locale.  Do you / how do you want to handle this in applications that use
Tribble outside the GATK?


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3917 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-08-03 03:48:26 +00:00
R A very nice way of automatically plotting the results of a VariantEval run. All of the hard work is actually in the common R repository, gsacommons.R, including methods for creating a Venn diagram. It also provides a mechanism for the output of a VariantEval run to be loaded into a single list object. 2010-07-19 12:38:26 +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 Coping out and forcing the entire GATK (and associated JVM) to use US English 2010-08-03 03:48:26 +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 Be smart about the headers. 2010-07-30 16:11:16 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +00:00
scala Slightly smarter interval list dealing (whole exome intervals are .interval_list, whole genome are .interval.list). Also use BTI with the Genomic Annotator 2010-07-29 22:04:02 +00:00
settings fix for a bug deep in the tribble indexing: if you had a single record in the first contig, the second contig's index blocks would point to the wrong file seek location, and you'd see no 2010-07-23 18:39:55 +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 A Java sizeof, implemented using the Java instrumentation API. Can either get the memory consumed either only by a single 2010-07-27 18:44:15 +00:00
ivy.xml adding the annotations for findbugs as dependencies in the GATK. They have to be in the default config so that we can 2010-07-19 16:34:57 +00:00