gatk3的最后一个经典版本3.8

delangel ece694d0af Next iteration on new UG framework: ... - Brought over exact AF estimation from branch (which is now dead). Exact model is default in UnifiedGenotyperV2. - Implemented completely new genotyping algorithm given best AF estimate using dynamic programming, which in theory should be better than both greedy search and any HWE-based genotyper. - Integrated and added new Dindel likelihood estimation model. - Corrected annotators that would call readBasePileup: since we can be annotating extended events, best way is to interrogate context for kind of pileup and either readBasePileup or readExtendedEventPileup. All changes above except last one are still in playground since they require more testing. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4396 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-30 21:33:59 +00:00
R	Ready for integration with queue script	2010-09-24 19:46:01 +00:00
archive	Cleaning up playground utils and tests	2010-08-27 01:25:47 +00:00
c	Reduce file handle usage.	2010-01-05 18:03:01 +00:00
doc	removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also	2010-08-19 00:42:37 +00:00
java	Next iteration on new UG framework:	2010-09-30 21:33:59 +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	Fix for DoC issue with multiplexer -- will retire use of multiplexer when	2010-09-07 00:44:07 +00:00
perl	Added 'Cron' to subject for easier message filtering	2010-09-28 21:03:50 +00:00
python	clean-up the docs a little	2010-09-29 05:02:41 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Be smarter if the beagle output is set such that getParent() returns null. Up the memory limit.	2010-09-30 12:48:47 +00:00
settings	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
shell	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +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	Moved the test classes from java/classes/testclasses to java/testclasses. Update your IntelliJ settings!	2010-09-30 20:42:41 +00:00
ivy.xml	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +00:00