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gatk3的最后一个经典版本3.8
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delangel 2ac938fe4e 1) 
Minor fixes to avoid crashes vs CG indel files:
- Add count for complex events, not just insertions and deletions
- Handle correctly cases of large indels falling out of bounds of histogram array: added a count of indels ouf of bounds and avoid exceptions.

2) Cosmetic fix for R script assessing UG calling performance: draw red y=x line on top of Simulated vs Estimated AC to get a better view of under/over-estimation of AC.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4758 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-11-30 21:08:25 +00:00
R 1) 2010-11-30 21:08:25 +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 1) 2010-11-30 21:08:25 +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 Updated the Queue GATK generator and packaging to include more dependencies for fullCallingPipeline.q. 2010-11-30 15:29:40 +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 calling pipeline for v13 of the paper calls -- the final version 2010-11-22 21:57:12 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Updated the Queue GATK generator and packaging to include more dependencies for fullCallingPipeline.q. 2010-11-30 15:29:40 +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 Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'. 2010-11-22 22:59:42 +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