gatk3的最后一个经典版本3.8

kshakir 7157cb9090 While bkill'ing on the shutdown thread Queue will no longer try to submit more jobs on the original thread. ... Updated pipeline output structure to current recommendations by Corin. Directories are now automatically before the function runs. Fixed several bugs with scatter gather binding when the script author needs to change the directories. Fixed bug with tracking of log files for CloneFunctions. More error handling and logging of exceptions (good test environment while LSF was down this early AM!) Removed cleanup utility for scatter gather. SG Output structure has changed significantly. Will need to discuss and find a better approach for Queue programatically deleting files. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4504 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-15 17:01:36 +00:00
R	Better reporting -- figured out how to drop unused levels in subset	2010-10-06 14:31:51 +00:00
archive	Cleaning up playground utils and tests	2010-08-27 01:25:47 +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	bug fix	2010-10-15 16:27:40 +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 all standard annotations	2010-10-11 20:52:08 +00:00
perl	updated liftover script: it no longer needs to re-sort the vcf	2010-10-15 08:03:41 +00:00
python	Adding a script to do big table conversion. Removing Ben's script which is totally obsolete and busted.	2010-10-12 01:40:43 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	While bkill'ing on the shutdown thread Queue will no longer try to submit more jobs on the original thread.	2010-10-15 17:01:36 +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	Fixes for example bam files	2010-10-05 18:43:02 +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	Wrapping ScatterGatherableFunctions with a facade instead of using slower clone library. Will require keeping Clone's facade code in sync with CommandLineFunction but runs *much* faster.	2010-10-07 01:19:18 +00:00
ivy.xml	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