gatk3的最后一个经典版本3.8

hanna b9cb57f4b9 A unit test is failing on bamboo in a way I can't reproduce (or even explain). ... Checking in some debugging info. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4916 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-31 16:35:04 +00:00
R	misc.	2010-12-22 20:16:41 +00:00
archive	Eric broke the build. Eric broke the build.	2010-12-15 17:01:38 +00:00
c	Bug fixes for the bwa aligner and changes to support compiling against newer releases of the bwa code base.	2010-12-17 14:49:15 +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	A unit test is failing on bamboo in a way I can't reproduce (or even explain).	2010-12-31 16:35:04 +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	Be certain to include core GATK reference metadata features and codecs in the	2010-12-21 21:30:07 +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 bug fixee, replace double quotes with single quotes in strings so that R can read the resulting table	2010-12-29 16:25:59 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Updating combien variants memory limit and dcov default for the full calling pipeline.	2010-12-24 03:06:50 +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	Better queue status messages	2010-12-22 20:17:28 +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