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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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hanna ee3f2eb1d0 Don't output traversal reduce result in the logger. In many cases, the reduce 
result is tangential to the product of the analysis and having the logger always
emit it can confuse the output (such as in the new reduceByInterval 
DepthOfCoverage walker).  If users want to emit it, they can choose not override
onTraversalDone, or override onTraversalDone and write results to the output
stream / logger / whatever their choice.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3422 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-05-23 22:41:43 +00:00
R Variant Optimizer accepts a dbSNP rod arugment to use in determining known/novel status as opposed to using the rsID in the vcf record. VO generates plots of annotation values used in clustering broken out by knowns and novels. Useful for showing which annotations are approximately Gaussian. 2010-05-09 16:48:07 +00:00
archive Retiring multi-sample genotyper 2010-05-20 14:11:11 +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 Don't output traversal reduce result in the logger. In many cases, the reduce 2010-05-23 22:41:43 +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 adding all of Tribble, not just select codecs, to the package 2010-05-21 15:48:50 +00:00
perl Add argument to sortByRef for specifying the tmp directory for sorting. 2010-05-07 13:53:26 +00:00
python minor change for eric 2010-05-21 20:13:36 +00:00
ruby Adding the ruby directory, and a simple script to restart Bamboo 2009-12-03 22:48:48 +00:00
scala/src A cleaned up functioning early, early access version of Queue for others to play with and provide feedback about next steps. 2010-05-23 20:21:09 +00:00
settings A cleaned up functioning early, early access version of Queue for others to play with and provide feedback about next steps. 2010-05-23 20:21:09 +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
LICENSE Adding a license to the root directory in case BOSC checks for one. Has the 2010-04-20 16:04:29 +00:00
build.xml A cleaned up functioning early, early access version of Queue for others to play with and provide feedback about next steps. 2010-05-23 20:21:09 +00:00
ivy.xml A cleaned up functioning early, early access version of Queue for others to play with and provide feedback about next steps. 2010-05-23 20:21:09 +00:00