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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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ebanks 6934f83cc7 Two changes to CombineVariants. 
1. Fix: VCs were padded before the merge, but they were never unpadded afterwards.  This leaves us with a VC that doesn't meet our spec.
2. Update: instead of running the merged VC through every standard annotation (which seems really wrong, since this isn't the annotator tool), just update the chromosome count annotations (AC,AF,AN) through VCUtils.



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4734 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-11-25 04:52:12 +00:00
R Useful profiling tool that reads in a single rod and evalutes the time it takes to read the file by byte, by line, into pieces, just the sites of the vcf, and finally the full vcf. Emits a useful table for plotting with the associated R script that can be run like Rscript R/analyzeRodProfile.R table.txt table.pdf titleString 2010-11-24 14:59:16 +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 Two changes to CombineVariants. 2010-11-25 04:52:12 +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 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 Adding a forgotten quote mark 2010-11-24 16:38:27 +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