gatk3的最后一个经典版本3.8

chartl 6db86ae0c6 PAC sets the refseq file to optional. ... Additional ipf for expanding interval lists. Either there's heavy latency on the toro -- or it's not working properly yet (e.g. the system print in the same scope as the file print outputs a line, but no file shows up on the system) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4874 348d0f76-0448-11de-a6fe-93d51630548a		2010-12-18 19:04:52 +00:00
R	Do not abort integration (over het-het distances) on errors, but warn about them	2010-12-16 17:20:25 +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	Now I call BeforeMethod correctly	2010-12-17 22:45:45 +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	Simplified the Queue package definition so that BCEL doesn't miss any dependent queue classes or those loaded via reflection.	2010-12-16 18:17:48 +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	Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers	2010-12-15 14:56:12 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	PAC sets the refseq file to optional.	2010-12-18 19:04:52 +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	Stabilitity improvements to GATK run report system. R code is now robust. XML parser uses the C backend in python, 10x faster. Added shell script that runs the daily reports, and linked the /humgen/ runme.csh to this script. Script now emails the group the daily PDFs to gsamembers	2010-12-15 14:56:12 +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