gatk3的最后一个经典版本3.8

ebanks 3aabc144c6 Added functionality to allow for a contract between LocusWindowTraversalEngine and LocusWindowWalker which allows the Walker to act upon reads outside of the provided intervals. ... (Really, all we want to do is spit out all reads, but this allows the Walker to do other things with the reads if it wants) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@641 348d0f76-0448-11de-a6fe-93d51630548a		2009-05-08 17:28:16 +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 functionality to allow for a contract between LocusWindowTraversalEngine and LocusWindowWalker which allows the Walker to act upon reads outside of the provided intervals.	2009-05-08 17:28:16 +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