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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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chartl fc33901810 Graph structure must be known at compile time. Removing GroupIntervals until a future point where in-process-functions can predict their output based on inputs [though this is probably forever: the inputs may not exist at compile time!] 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4886 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-12-20 21:22:58 +00:00
R Return analyzed window sizes as well 2010-12-20 17:00:17 +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 No longer emits records at filtered sites, in sub-sampling mode 2010-12-20 16:43:50 +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 Simplified the Queue package definition so that BCEL doesn't miss any dependent queue classes or those loaded via reflection. 2010-12-16 18:17:48 +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 Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers 2010-12-15 14:56:12 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Graph structure must be known at compile time. Removing GroupIntervals until a future point where in-process-functions can predict their output based on inputs [though this is probably forever: the inputs may not exist at compile time!] 2010-12-20 21:22:58 +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 Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers 2010-12-15 14:56:12 +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