gatk3的最后一个经典版本3.8

jmaguire 641afc4e76 fix a crash in the event that the input file has no read groups! ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@714 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-14 19:27:41 +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	fix a crash in the event that the input file has no read groups!	2009-05-14 19:27:41 +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 to latest.	2009-05-13 19:19:55 +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	Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit.	2009-05-13 21:32:05 +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