gatk-3.8

gatk3的最后一个经典版本3.8

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aaron 0108517b98 updating the Tribble track loading code to use the new shared locks, updated lots of new tests, add infrastructure for the TreeInterval, and removed the old locking class. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3837 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-20 07:08:10 +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	1. Refactoring of GenoypeWriters so that parallelization now works again with VCF4.0. We now have just a single reference to the old VCF classes, and that one will be purged soon.	2010-07-20 06:16:45 +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	updating the Tribble track loading code to use the new shared locks, updated lots of new tests, add infrastructure for the TreeInterval, and removed the old locking class.	2010-07-20 07:08:10 +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	Add CountFunctionalVariants to local release (for firehose)	2010-07-17 01:36:16 +00:00
perl	1. Updated tests and added integration test for liftover code.	2010-07-12 17:58:18 +00:00
python	Improvements to 1KG processing pipeline	2010-07-16 15:33:47 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala	1KG Table 1 counting pipeline. Useful example	2010-07-17 22:30:56 +00:00
settings	updating the Tribble library; added writing of indexes to the index interface for working with the tree index.	2010-07-20 07:02:08 +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 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