gatk3的最后一个经典版本3.8

depristo f3f5e849cb SSG now in early access ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1581 348d0f76-0448-11de-a6fe-93d51630548a		2009-09-10 16:45:19 +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	So, the VCF spec allows for an optional meta field in the header representing the date. However, using this field means that integration tests run on the vcf file will fail the MD5 test (which is what happened to the VariantFiltration test this morning after working just fine yesterday).	2009-09-10 14:28:43 +00:00
packages	SSG now in early access	2009-09-10 16:45:19 +00:00
perl	A useful perl module for quick argument parsing.	2009-08-31 15:44:57 +00:00
python	better feedback now	2009-09-10 12:43:45 +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