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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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kshakir 79725f2d9c Excluding the QFunction log files from the set of files to delete on completion. 
When a QGraph is empty displaying a warning instead of crashing with an JGraph internal assertion error.
Cleaned up code using the Log4J root logger and explicitly talking to a logger for Sting.
When integration tests are run detecting that the logger has already been setup so that messages aren't logged twice.
Updated from Ivy 2.2.0-rc1 to 2.2.0.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4707 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-11-18 20:22:01 +00:00
R Actually subsets the resulting table now, like it was supposed to all along. 2010-11-17 16:18:23 +00:00
archive Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct. 2010-10-22 20:35:53 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also 2010-08-19 00:42:37 +00:00
java Excluding the QFunction log files from the set of files to delete on completion. 2010-11-18 20:22:01 +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 Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release. 2010-11-18 02:33:45 +00:00
perl Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release. 2010-11-18 02:33:45 +00:00
python V1 of the data processing paper, produced results for the manuscript we presented. Commit for archival purposes 2010-11-11 01:43:21 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Excluding the QFunction log files from the set of files to delete on completion. 2010-11-18 20:22:01 +00:00
settings Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline. 2010-10-14 15:58:52 +00:00
shell Useful script for me 2010-11-18 15:21:06 +00:00
testdata VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary 2010-11-15 22:19:22 +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 Excluding the QFunction log files from the set of files to delete on completion. 2010-11-18 20:22:01 +00:00
ivy.xml Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader. 2010-11-12 20:14:28 +00:00