gatk3的最后一个经典版本3.8

aaron 898f65547e Added code to split GenomeAnalysisTK.java into an object concerned with loading command line args, and one that runs the engines. This will allow us to run the GATK from other tools (like Matlab). Also some cleanup to seperate out the legacy traversals and the new style traversals. This is not live yet, and any modifications you need should be made to GenomeAnalysisTK.java for now. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@650 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-11 02:07:20 +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 split GenomeAnalysisTK.java into an object concerned with loading command line args, and one that runs the engines. This will allow us to run the GATK from other tools (like Matlab). Also some cleanup to seperate out the legacy traversals and the new style traversals. This is not live yet, and any modifications you need should be made to GenomeAnalysisTK.java for now.	2009-05-11 02:07:20 +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	Added BCEL and some basic instrumenation code to the test library.	2009-05-06 17:18:23 +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