gatk3的最后一个经典版本3.8

ebanks 42eb356782 1. modifed by read traversals with indexes to be more general ... 2. GenomeLocs for reads should have ends spanning the read (moved it to GenomeLoc from Utils) 3. Got rid of those stupid unmappable characters from comments in various files git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@289 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-03 18:24:08 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	rod's now have names. Use getName() to access it. Next step is better interface to accessing rods	2009-04-03 16:41:33 +00:00
java	1. modifed by read traversals with indexes to be more general	2009-04-03 18:24:08 +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	Bump picard and samtools to latest.	2009-03-27 02:26:28 +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	Removed now-useless FourBaseCaller jar target (FourBaseRecaller replaces it).	2009-04-02 22:13:51 +00:00
ivy.xml	Bump picard and samtools to latest.	2009-03-27 02:26:28 +00:00