gatk3的最后一个经典版本3.8

hanna f18ac069e2 A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup. ... Provides a cleaner interface with extended events inheriting all of the basic RBP functionality. Implementation is still slightly messy, but should allow users to provide separate implementations of methods for sample split pileups and unsplit pileups for efficiency's sake. Methods not covered by unit/integration tests have not been sufficiently tested yet. Unit tests will follow this week. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3597 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-20 04:42:26 +00:00
R	This script produces tearsheet and data processing report figures and tables when given Squid and Firehose produced data	2010-06-18 21:36:29 +00:00
archive	Retiring multi-sample genotyper	2010-05-20 14:11:11 +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	A refactoring / unification of ReadBackedPileup and ReadBackedExtendedEventPileup.	2010-06-20 04:42:26 +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	Update to the latest rev of the picard sharding patch. Includes updates reflecting	2010-06-06 20:33:21 +00:00
perl	Stupid cent_os doesn't allow old style 'sort' conventions. Updating liftover script...	2010-06-17 13:44:03 +00:00
python	Fixed typo	2010-06-15 21:17:14 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala/src	Fix for a reflection issue with generic types.	2010-06-16 15:58:38 +00:00
settings	GATK now uses a optimized indexing scheme in Tribble. 5x or more performance gain on files with many genotypes. Updated integrationtest that was failing and was clearly wrong. DB=; isn't a valid annotation.	2010-06-19 21:36:41 +00:00
shell	Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls *AND* the compares the geli MD5 sum to the expected one!	2009-09-04 12:39:06 +00:00
testdata	a small dbsnp file for Tribble testing	2010-02-18 18:12:55 +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	Removing these utilities as part of a hostage negotation with Matt. Can I have my journal club paper now?!	2010-06-11 21:41:29 +00:00
ivy.xml	Replaced pattern matched pipeline spec with annotated objects.	2010-06-15 04:43:46 +00:00