gatk3的最后一个经典版本3.8

hanna 0f3049652a Start to build BWT abstractions, so we can present a reasonable facsimile of the BWT to the user no matter how it's represented on disk. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1589 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-11 18:23:15 +00:00
R	Updated python files	2009-07-07 14:15:39 +00:00
c	Move non-java code out of playground.	2009-03-23 19:31:38 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	Start to build BWT abstractions, so we can present a reasonable facsimile of the BWT to the user no matter how it's represented on disk.	2009-09-11 18:23:15 +00:00
packages	SSG now in early access	2009-09-10 16:45:19 +00:00
perl	Some useful scripts for running only individual parts of the pilot1/2 cleaning/calling pipeline	2009-09-11 17:38:33 +00:00
python	Fix merger command	2009-09-11 13:13:23 +00:00
scala/src	support for scala walkers	2009-08-28 00:15:01 +00:00
settings	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +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	change to make build work	2009-09-03 13:43:10 +00:00
build.xml	changes to the variation class, updates to SSG, updated tests based on changes to the SSGenotypeCall, and added the ability to run a single integration test from using the build script.	2009-09-10 04:31:33 +00:00
ivy.xml	Switched to Reflections (http://code.google.com/p/reflections/) project for	2009-07-21 18:32:22 +00:00