gatk-3.8

gatk3的最后一个经典版本3.8

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ebanks b9a59ea54f Adding Het/Hom ratio to the temp per sample metrics. Because I'm in a generous mood tonight, I'm going ahead and fixing the paths for the classes I'm touching... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4713 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-21 04:24:42 +00:00
R	Actually subsets the resulting table now, like it was supposed to all along.	2010-11-17 16:18:23 +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	Adding Het/Hom ratio to the temp per sample metrics. Because I'm in a generous mood tonight, I'm going ahead and fixing the paths for the classes I'm touching...	2010-11-21 04:24:42 +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	V1 of the data processing paper, produced results for the manuscript we presented. Commit for archival purposes	2010-11-11 01:43:21 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Putting the annotation back in, both to the filters and to UG	2010-11-18 21:02:15 +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	Excluding the QFunction log files from the set of files to delete on completion.	2010-11-18 20:22:01 +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