gatk3的最后一个经典版本3.8

kshakir 75c98c42b8 Started path of deprecation of Sting's @Argument by splitting the annotation into @Output and @Input. Anything that's not an @Output should be an @Input. ... Checked in example qscripts that are basically todo integration tests. Replaced use of queue @Input/@Output with Sting's new @Input/@Output. This means you'll now have to doc-ument the annotations. More work on dependency resolution cycles being created in the graph during scatter/gather. Filtering nulls to avoid NPE exceptions in scala's 'Collection'.hashCode. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3643 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-25 20:51:13 +00:00
R	This replaces tearsheet.r, neatens up graphics, and allows the script to be used in R's interactive environment	2010-06-24 01:02:58 +00:00
archive	Retiring multi-sample genotyper	2010-05-20 14:11:11 +00:00
c	Reduce file handle usage.	2010-01-05 18:03:01 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	Started path of deprecation of Sting's @Argument by splitting the annotation into @Output and @Input. Anything that's not an @Output should be an @Input.	2010-06-25 20:51:13 +00:00
matlab	Another matlab script -- this time for making power and coverage plots over a specific gene region. Lots of fun file reading, string manipulation, and exploration of the set() function	2009-11-30 20:02:25 +00:00
packages	Update to the latest rev of the picard sharding patch. Includes updates reflecting	2010-06-06 20:33:21 +00:00
perl	bug fix: now contigs not present in the sequence dictionary are registered properly and do not cause the script to break	2010-06-23 20:59:38 +00:00
python	Fixed -t arg	2010-06-24 23:44:10 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala	Started path of deprecation of Sting's @Argument by splitting the annotation into @Output and @Input. Anything that's not an @Output should be an @Input.	2010-06-25 20:51:13 +00:00
settings	Rev'ing Tribble with a special version that has excluded VCF 3.3	2010-06-25 18:20:51 +00:00
shell	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00
testdata	and add changes to the vcf used in testing	2010-06-25 02:56:02 +00:00
LICENSE	Adding a license to the root directory in case BOSC checks for one. Has the	2010-04-20 16:04:29 +00:00
build.xml	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00
ivy.xml	Refactoring for a first version of scatter gather api with basic shell script implementations.	2010-06-22 18:39:20 +00:00