gatk3的最后一个经典版本3.8

kiran 28c1330b4b Fixed a bug wherein the loop variable for the second end of the pair was actually looping over the entire raw read (first and second ends combined). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@178 348d0f76-0448-11de-a6fe-93d51630548a		2009-03-24 21:59:25 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Changed how the example walker gets run, I'm about to check in the GNU style command line args.	2009-03-22 20:10:17 +00:00
java	Fixed a bug wherein the loop variable for the second end of the pair was actually looping over the entire raw read (first and second ends combined).	2009-03-24 21:59:25 +00:00
python	Added Hapmap data track (using rodGFF class for GFF file format) to toolkit as a command line option, Hapmap metrics to AlleleFrequencyMetricsWalker, and a python Geli2GFF file converter.	2009-03-24 03:58:03 +00:00
settings	Update picard to work with new samtools.	2009-03-20 21:51:26 +00:00
shell	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
testdata	Skeleton of new directory structure.	2009-03-11 20:05:05 +00:00
build.xml	added some cleanup of code, and new junit targets to the build file	2009-03-24 21:16:12 +00:00
ivy.xml	Switched our code over to the new command line style (gnu style args), added the initial logger code, and added apache commons CLI to the IVY script.	2009-03-22 21:06:22 +00:00