gatk3的最后一个经典版本3.8

delangel b6bdd61283 a) Fix bug when multi-base reference is homopolymeric when writing a VCF4.0 variant context: computation of number of trailing bases was incorrect and we ended up with incorrect position. ... b) Updated VCF4WriterTestWalker to take either VCF3 or VCF4 as inputs (this walker can also be used to convert from 3.3 to 4.0). git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3711 348d0f76-0448-11de-a6fe-93d51630548a		2010-07-02 15:19:42 +00:00
R	useful routines for R	2010-06-30 16:38:49 +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) Fix bug when multi-base reference is homopolymeric when writing a VCF4.0 variant context: computation of number of trailing bases was incorrect and we ended up with incorrect position.	2010-07-02 15:19:42 +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	Updated to reflect Mark's renaming binge	2010-06-30 22:48:42 +00:00
python	misc. useful updates to python library	2010-06-30 16:33:32 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala	Checking in a simplistic VR qscript file for posterity's sake	2010-07-01 18:53:17 +00:00
settings	Rev Picard with new IndexedFastaSequenceFile patch.	2010-07-01 03:05:43 +00:00
shell	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +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	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00
ivy.xml	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00