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gatk3的最后一个经典版本3.8
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ebanks cb31d5a0ab VariantFiltration now outputs VCF. Important changes: 
1. VariantsToVCF can now be called statically to output VCF for a single ROD instance; this is temporary until we have a VCF ROD.
2. VariantFiltration now outputs only 2 files, both mandatory: all variants that pass filters in geli text, and all variants in VCF.
If there are any problems, go find Aaron.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@1569 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-09-09 20:04:32 +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 VariantFiltration now outputs VCF. Important changes: 2009-09-09 20:04:32 +00:00
packages Added VariantFiltrationWalker to GATK early release. 2009-09-02 02:17:50 +00:00
perl A useful perl module for quick argument parsing. 2009-08-31 15:44:57 +00:00
python LocusIterationByState is now the system deafult. Fixed Aaron's build problem 2009-09-09 01:28:05 +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 bug fixes to LIBS and LIBH following ultra-aggressive regression testing across 454, solid, and solexa 2009-09-09 15:36:12 +00:00
ivy.xml Switched to Reflections (http://code.google.com/p/reflections/) project for 2009-07-21 18:32:22 +00:00