gatk3的最后一个经典版本3.8

kiran ecd496cf51 Modifications to reflect changes to gsalib. Smarter about figuring out the names of the filtered parts of the callset. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4739 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-27 23:26:03 +00:00
R	Modifications to reflect changes to gsalib. Smarter about figuring out the names of the filtered parts of the callset.	2010-11-27 23:26:03 +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	Looking over the daily error log email made me realize that there were 2 implementations of vc.modifyLocation() - the correct one in VC that didn't require lazy loading the genotype data and the bad one in VCUtils that did. Removing the implementation in VCUtils and updating the code accordingly. Also, removing createPotentiallyInvalidGenomeLoc() since no one uses it anymore.	2010-11-26 18:40:34 +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	Added a ten sample 1000G whole exome test along with SimpleMetricsBySample to the pipeline validation.	2010-11-26 23:17:23 +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