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gatk3的最后一个经典版本3.8
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ebanks ee0e833616 Some significant changes to the annotator: 
1. Annotations can now be "decorated" with any arbitrary interface description - not just standard or experimental.
2. Users can now not only specify specific annotations to use, but also the interface names from #1.  Any number of them can be specified, e.g. -G Standard -G Experimental -A RankSumTest.
3. These same arguments can be used with the Unified Genotyper for when it calls into the Annotator.
4. There are now two types of annotations: those that are applied to the INFO field and those that are applied to specific genotypes (the FORMAT field) in the VCF (however, I haven't implemented any of these latter annotations just yet; coming soon).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3029 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-03-18 05:38:32 +00:00
R Variant optimizer now outputs VCF files via ApplyVariantClustersWalker. Documentation to be added to the wiki. It is ready to be used by other people but only with great caution. 2010-03-17 20:41:42 +00:00
archive moving older versions of the oneoff project to archive, bye-bye 2010-02-04 19:46:27 +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 Some significant changes to the annotator: 2010-03-18 05:38:32 +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 removing a reference to the VCFValidator, which is gone. 2010-03-11 21:32:17 +00:00
perl Passing just the single alternate allele to the converted maf on the recommendation of mike lawrence and kiran. 2010-03-17 19:08:37 +00:00
python automatic generation of individual and individual set import files 2010-03-15 10:36:33 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +00:00
scala/src Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar. 2009-11-02 06:02:41 +00:00
settings adding a stripped down Tribble library for the start of integration 2010-02-17 21:29:25 +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
build.xml In the new sharding system, if no read group is present, hallucinate one. Added 2010-03-07 23:01:34 +00:00
ivy.xml adding a stripped down Tribble library for the start of integration 2010-02-17 21:29:25 +00:00