gatk3的最后一个经典版本3.8

kiran eb1bb94d1c Moved the evaluation of the JEXL expressions to a point *after* the samples are subset and the INFO-field annotations are updated. I think this makes more sense than having the evaluations happen beforehand, since it seems jarring to have the JEXL expressions operate on the annotations before they're updated, and have the file contain the annotations after they're updated. Now, selecting on something like allele frequency will actually apply to the annotations that actually end up in the file, while selection on other annotations (which are carried over without modification) will act exactly the same regardless. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3970 348d0f76-0448-11de-a6fe-93d51630548a		2010-08-08 04:09:02 +00:00
R	Publication tranches report is now the default output	2010-08-07 13:58:59 +00:00
archive	Archiving	2010-07-27 02:47:18 +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	Moved the evaluation of the JEXL expressions to a point *after* the samples are subset and the INFO-field annotations are updated. I think this makes more sense than having the evaluations happen beforehand, since it seems jarring to have the JEXL expressions operate on the annotations before they're updated, and have the file contain the annotations after they're updated. Now, selecting on something like allele frequency will actually apply to the annotations that actually end up in the file, while selection on other annotations (which are carried over without modification) will act exactly the same regardless.	2010-08-08 04:09:02 +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	Updated resources package descriptor with dbsnp 129 for b37.	2010-08-03 02:42:48 +00:00
perl	1. Updated tests and added integration test for liftover code.	2010-07-12 17:58:18 +00:00
python	now support -o output option, useful for pipelines	2010-08-06 14:57:04 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala	Switch to newer version of comp tracks (and make the trigger track a comp as well). Indel cleaning should override the interval list and only use the contig interval list; and also force jobs to go to long.	2010-08-04 20:05:27 +00:00
settings	fix for a bug deep in the tribble indexing: if you had a single record in the first contig, the second contig's index blocks would point to the wrong file seek location, and you'd see no	2010-07-23 18:39:55 +00:00
shell	Useful script to see the status of gsa computing resources. Crontab'd and will be arriving as email at 8 am	2010-08-07 12:36:28 +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	VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:	2010-08-05 18:47:53 +00:00
ivy.xml	VariantContext has now moved over to Tribble, and the VCF4 parser is now the only VCF parser in town. Other changes include:	2010-08-05 18:47:53 +00:00