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gatk3的最后一个经典版本3.8
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257 MiB
Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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kshakir 9923e05e0a Moved MD5 utils from WalkerTest to BaseTest for use by PipelineTests. 
Moved VariantEval validation from FCPTest to PipelineTest.
Cleaned up some duplicate code for writing temp files during tests.
Moved FCPTest to playground namespace to match move for FCP.q.
Added a basic HelloWorldPipelineTest for the HelloWorld QScript. 
Moved duplicated error handling from JobRunners into the FunctionEdge.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5068 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-01-25 04:11:49 +00:00
R Updating the file path for proper inclusion of the background in the tearsheet. 2011-01-22 19:15:33 +00:00
analysis/depristo/distributedGATK V3 of the distributed GATK. High-efficiency implementation. Support for status tracking for debugging and display. Still not safe for production use due to NFS filelock problem. V4 will use alternative file locking mechanism 2011-01-24 16:45:07 +00:00
archive Moving GLF code to archive 2011-01-15 22:42:42 +00:00
c Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base. 2010-12-17 14:49:15 +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 Moved MD5 utils from WalkerTest to BaseTest for use by PipelineTests. 2011-01-25 04:11:49 +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 the native jna support libraries from the jna.jar to the Queue package jar. 2011-01-08 10:48:30 +00:00
perl Fixed bug that required users to use the recordOriginalLocation option 2011-01-05 23:12:14 +00:00
python Deleting old python code 2011-01-07 21:33:45 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Moved MD5 utils from WalkerTest to BaseTest for use by PipelineTests. 2011-01-25 04:11:49 +00:00
settings Update Picard / sam-jdk at Tim's request. 2011-01-03 02:17:25 +00:00
shell V3 of the distributed GATK. High-efficiency implementation. Support for status tracking for debugging and display. Still not safe for production use due to NFS filelock problem. V4 will use alternative file locking mechanism 2011-01-24 16:45:07 +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 FASTQ directory is gone 2011-01-13 15:16:06 +00:00
ivy.xml Adding lucene dependency for file locking -- may be removed in the near future 2011-01-24 18:59:42 +00:00