gatk3的最后一个经典版本3.8

kshakir 8ba3a5a43f Command lines for locally run Queue jobs no longer have to be escaped differently than bsub'ed jobs. ... GSA-410 Local job runs now can run command lines longer than than 4096 on our linux machines. When determining if the help text and Queue extensions need to be rebuilt, use the .class files not the .java so that GATK oneoffs are picked up correctly. Added the most basic of all example QScripts for debugging, Hello World. Minor updates to copy/pasted LSF code to reduce ant javadoc warnings by a third. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4970 348d0f76-0448-11de-a6fe-93d51630548a		2011-01-10 21:07:29 +00:00
R	Private mutation simulator and analysis routines for EOMI paper	2011-01-07 21:23:29 +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	Command lines for locally run Queue jobs no longer have to be escaped differently than bsub'ed jobs.	2011-01-10 21:07:29 +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	Adding the native jna support libraries from the jna.jar to the Queue package jar.	2011-01-08 10:48:30 +00:00
perl	Fixed bug that required users to use the recordOriginalLocation option	2011-01-05 23:12:14 +00:00
python	Deleting old python code	2011-01-07 21:33:45 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Command lines for locally run Queue jobs no longer have to be escaped differently than bsub'ed jobs.	2011-01-10 21:07:29 +00:00
settings	Update Picard / sam-jdk at Tim's request.	2011-01-03 02:17:25 +00:00
shell	watch -n 30 shell/pipelineJobs.csh for those who want to watch the gsaadm's jobs progress	2011-01-09 13:09:30 +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	Command lines for locally run Queue jobs no longer have to be escaped differently than bsub'ed jobs.	2011-01-10 21:07:29 +00:00
ivy.xml	Removed stochasticity from IndelRealigner by random sampling using and seed based on the read list.	2011-01-07 22:03:36 +00:00