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gatk3的最后一个经典版本3.8
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ebanks 0097106938 VariantFiltration can now filter specific samples. 
This is *NOT* an ideal implementation.  One day when we have lots of free time (or a greater desire), we will implement this correctly and sophisticatedly using all the power of JEXL.  For now, though, this will have to do.
Docs coming tonight.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3060 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-03-22 20:45:11 +00:00
R Minor updates to output of variant optimizer. 2010-03-18 12:46:47 +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 VariantFiltration can now filter specific samples. 2010-03-22 20:45:11 +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 updating the package 2010-03-19 13:42:31 +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 better farm commands, and simple utility to convert ucsc repeat masks to interval lists 2010-03-19 13:11:06 +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 Up the svn revision number in an attempt to force an update, again due to an 2010-03-19 22:39:56 +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 dependency that I forgot. 2010-03-18 13:32:37 +00:00