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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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depristo d31c658c2e Organized performance monitoring passes unit tests and is more efficient 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4924 348d0f76-0448-11de-a6fe-93d51630548a
 		2011-01-03 02:09:08 +00:00
R --performanceLog (-PF) X.dat argument now enabled. Writes out a table (R-friendly) of the performance of the GATK over time, exactly as a more detailed version of the INFO progress meter. R script for useful plotting of the performance of the GATK over time. Will be helpful for upcoming scalability testing and debugging of memory leaks and other incremental performance problems 2011-01-02 23:34:21 +00:00
archive Eric broke the build. Eric broke the build. 2010-12-15 17:01:38 +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 Organized performance monitoring passes unit tests and is more efficient 2011-01-03 02:09:08 +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 Be certain to include core GATK reference metadata features and codecs in the 2010-12-21 21:30:07 +00:00
perl A helper script to merge two VCFs, run VariantEval, and the VariantReport.R script. 2010-11-28 00:45:21 +00:00
python no longer prints unnecessary table conversion failures that muck up emails. Run script now uses du not ls to display archive size 2011-01-02 13:27:37 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Updating combien variants memory limit and dcov default for the full calling pipeline. 2010-12-24 03:06:50 +00:00
settings Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
shell no longer prints unnecessary table conversion failures that muck up emails. Run script now uses du not ls to display archive size 2011-01-02 13:27:37 +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 Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00
ivy.xml Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +00:00