gatk3的最后一个经典版本3.8

aaron 9f942fdfa0 Added code to correct the violation of the parsing interface. Now the analysis type resides in the command line arg, but is stored into the argument collection before it's passed to the genomeAnalysisEngine. ... Also fixed a bug where we'd exception-out if we didn't provide a interval region. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@669 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-12 15:33:55 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Provide a default logger, some config settings, and some doc updates.	2009-04-29 02:06:05 +00:00
java	Added code to correct the violation of the parsing interface. Now the analysis type resides in the command line arg, but is stored into the argument collection before it's passed to the genomeAnalysisEngine.	2009-05-12 15:33:55 +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	Switch over to the GenomeAnalysisEngine/CommandLineGATK system from the GenomeAnalysisTK code.	2009-05-11 22:05:58 +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