gatk-3.8

gatk3的最后一个经典版本3.8

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kiran d492eb94ad Actually subsets the resulting table now, like it was supposed to all along. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4696 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-17 16:18:23 +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	JEXL expressions now generate exceptions, not warnings. Tools should catch the runtime exception to handle correctly. Removed unncessary complexity from the JEXL contexts	2010-11-17 16:08:16 +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	include the codecs into the RMD indexer that are available in the GATK, not just Tribble	2010-11-11 06:35:04 +00:00
perl	Script based on the second part of Eric's createTranscriptToGenomicInfoTables.pl script which sorts flat files by reference order	2010-11-15 19:44:32 +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	Fixing a silly typo	2010-11-15 18:16:51 +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	Inprocess functions by default now log what output files they are running for.	2010-10-07 19:08:02 +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	- Reintroduce test dependency so that the tests passing / failing is not	2010-11-16 19:55:20 +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