gatk3的最后一个经典版本3.8

kcibul ce72932a45 * refactored GenomeLoc to use contigIndex internally for performance and fixed several calling classes ... * added basic unit test for GenomeLoc * fixed bug when parsing genome locations like chr1:5000 the start position was being left as maxint rather than being set to the same as the stop position. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@365 348d0f76-0448-11de-a6fe-93d51630548a		2009-04-12 02:25:17 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	Updated with last week / next week for 6 April.	2009-04-06 14:05:20 +00:00
java	* refactored GenomeLoc to use contigIndex internally for performance and fixed several calling classes	2009-04-12 02:25:17 +00:00
python	Helper utility for merging BAM files	2009-04-09 20:10:41 +00:00
settings	Bump sam jdk to svn rev 207.	2009-04-08 22:16:46 +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	Initial test suite for FastaSequenceFile2, so I can add parallelism support with abandon.	2009-04-11 21:10:42 +00:00
ivy.xml	Added castor dependency.	2009-04-07 22:27:39 +00:00