gatk3的最后一个经典版本3.8

aaron 6db9127f90 Added changes to shattering, refactored SAMBAM into SAM ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@426 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-15 13:52:56 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Updated with last week / next week for 6 April.	2009-04-06 14:05:20 +00:00
java	Added changes to shattering, refactored SAMBAM into SAM	2009-04-15 13:52:56 +00:00
python	General purpose pileup code -- you can use these features to obtain detailed pileup data from reads and offsets. Useful for all pileup based walkers. Expanded support for rodSAMPileup to enable the new ValidatingPileupWalker, which takes a samtools pileup output and checks that GATK gives identical output as samtools on a per base and per qual pileup. It's going to be a very useful validation tool.	2009-04-14 22:13:10 +00:00
settings	Bump sam jdk to svn rev 207.	2009-04-08 22:16:46 +00:00
shell	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
testdata	Skeleton of new directory structure.	2009-03-11 20:05:05 +00:00
build.xml	Added the base test case, fixed the rest of the test cases to follow suit. Added more verbose output to ant for junit tests.	2009-04-14 17:11:38 +00:00
ivy.xml	Added castor dependency.	2009-04-07 22:27:39 +00:00