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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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delangel 17db2e0e24 (forgot I hadn't committed this) - refactored IndelStatistics module and added a new inner class to compute Indel classification along with other statistics. So, we now get an extra table specifying, per sample, counts of whether indels are: 
- Repeat Expansions
- Novel sequence
And for indels of size <=2 we get a per-mononuc. or dinuc. breakdown of novels and expansions.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4828 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-12-13 17:43:43 +00:00
R Default R script now plots sensitivity/specificity curve 2010-12-13 16:55:11 +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 Switched from LSF command line wrappers to JNA wrappers around the C API. Side effects: 2010-12-10 04:36:06 +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 (forgot I hadn't committed this) - refactored IndelStatistics module and added a new inner class to compute Indel classification along with other statistics. So, we now get an extra table specifying, per sample, counts of whether indels are: 2010-12-13 17:43:43 +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 Minor improvements to my crappy old python job management system. Mauricio's first task is to retire all of this code and move the DPP pipeline over to Queue 2010-12-09 04:44:16 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala In-process versions of sample extraction and interval-list conversion for VCF files. Required an in-process-function branch of the queue library. 2010-12-13 17:36:53 +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 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 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