gatk3的最后一个经典版本3.8

aaron 9579aace1f updates to code dependent on Tribble, as well as the following Tribble changes: ... - makes writing to disk optional for indexes using the indexCreator classes (allow the user to specify the index file, if null don't write it) - removed some system.out debugging code - fixed version checking in interval tree - made indexes store and return a LinkedHashSet for sequence names (to ensure they've preserved the ordering in the file) - index creators now read the file before creating the index - changed the Index.write() method to take a LEDataStream instead of a file - removed the sequence dictionary code on the header - added utils for getting LEDataStreams - added a base Tribble exception git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3857 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-23 01:56:10 +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	updates to code dependent on Tribble, as well as the following Tribble changes:	2010-07-23 01:56:10 +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	module for listing out samples for data processing and firehose reporting	2010-07-21 15:05:41 +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	updates to code dependent on Tribble, as well as the following Tribble changes:	2010-07-23 01:56:10 +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