gatk3的最后一个经典版本3.8

aaron 5725de56dc fixes in VCF, some changes to get it ready to move out of the GATK ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1441 348d0f76-0448-11de-a6fe-93d51630548a		2009-08-19 23:31:03 +00:00
R	Updated python files	2009-07-07 14:15:39 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	fixes in VCF, some changes to get it ready to move out of the GATK	2009-08-19 23:31:03 +00:00
packages	Added indel cleaner and quality scores recalibrator to the GATK package.	2009-07-24 16:20:38 +00:00
perl	Now you can specify '-' instead of input file name, and the script will read from stdin	2009-08-14 20:30:56 +00:00
python	I've pulled out the functionality of the analyzer into a single python file which doesn't require all of the irrelevant config parameters (which would cause problems for external users). I'll release this and the simple config file to 1KG for use in analyzing recalibration efforts.	2009-08-11 02:56:43 +00:00
settings	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +00:00
shell	Version 0.2.1 (released) of the TableRecalibrator	2009-06-25 22:50:55 +00:00
testdata	2009_02 release is no longer with us. Update the bam list.	2009-08-11 12:49:23 +00:00
build.xml	Exclude secondary base caller code from playground jar. Still TODO: figure	2009-07-30 21:02:46 +00:00
ivy.xml	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +00:00