gatk-3.8

gatk3的最后一个经典版本3.8

Go to file

aaron dde93e743f always output a brief test summary to the screen, and xml to disk git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3535 348d0f76-0448-11de-a6fe-93d51630548a		2010-06-11 16:24:50 +00:00
R	Automatic cutting of recalibrated variant calls using ApplyVariantCuts. VariantRecalibrator produces the tranches plot alongside the optimization curve. Specify the levels using -tranche 1.0 -tranche 5.0 etc	2010-06-02 15:03:00 +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	Adding "abi_solid" to the list of known platforms.	2010-06-11 13:37:19 +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	A script to sanity check that a release is runnable.	2010-05-26 17:45:42 +00:00
python	Added -w filter option allowing user to specify chromosomes to be skipped.	2010-06-10 20:58:25 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala/src	Multiple inputs / outputs for rules.	2010-05-30 08:28:16 +00:00
settings	re-updating the VCF code to handle spaces in sample names	2010-06-10 20:18:34 +00:00
shell	Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls AND the compares the geli MD5 sum to the expected one!	2009-09-04 12:39:06 +00:00
testdata	a small dbsnp file for Tribble testing	2010-02-18 18:12:55 +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	always output a brief test summary to the screen, and xml to disk	2010-06-11 16:24:50 +00:00
ivy.xml	JEXL2 upgrade. Improvements to JEXL processing including dynamically resolving variable -> value bindings instead of up front adding them to a map. Performance improvements and code cleanup throughout.	2010-06-07 00:33:02 +00:00