gatk3的最后一个经典版本3.8

aaron 5f924c46e0 Added documentation for calling the GATK from Matlab. This is to document the extreme basic and experimental support for using Matlab to call the GATK, and is more of a placeholder for when we have time to revisit supporting this. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@687 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-13 15:25:51 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Added documentation for calling the GATK from Matlab. This is to document the extreme basic and experimental support for using Matlab to call the GATK, and is more of a placeholder for when we have time to revisit supporting this.	2009-05-13 15:25:51 +00:00
java	fixing kiran's busted build	2009-05-12 21:29:04 +00:00
python	Reference-ordered data relies on bugs in the old command-line argument system to work. Update the ROD system to from -B track1 type1 file1 track2 type2 file2 to -B track1,type1,file1 -B track2,type2,file2.	2009-05-08 15:28:19 +00:00
settings	Bumped sam-jdk version to fix bug unzipping bam files.	2009-04-28 20:02:05 +00:00
shell	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
testdata	Better validation scripts and data	2009-04-29 17:40:07 +00:00
build.xml	Moved secondary base stuff out of playground for the purpose of making it a core utility. Modified package names and imports such that things would build properly.	2009-05-12 20:24:18 +00:00
ivy.xml	Change the sample XML marshalling code over to simple XML, and take out the castor lines in the ivy.xml	2009-05-08 00:08:25 +00:00