gatk3的最后一个经典版本3.8

depristo 8c16babe91 continuing improvements to the queueStatus helper script ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4261 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-12 14:04:59 +00:00
R	Removed unused dependency (it was causing a problem by looking for an X11 connection that didn't necessarily exist).	2010-09-09 19:56:00 +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	Penultimate step in exception system overhaul. UserError is now UserException. This class should be used for all communication with the USER for problems with their inputs. Engine now validates sequence dictionaries for compatibility, detecting not only lack of overlap but now inconsistent headers (b36 ref with v37 BAM, for example) as well as ref / bam order inconsistency. New -U option to allow users to tolerate dangerous seq dict issues. WalkerTest system now supports testing for exceptions (see email and wiki for docs). Tests for vcf and bam vs. ref incompatibility. Waiting on Tribble seq dict improvements to detect b36 VCF with b37 ref (currently cannot tell this is wrong.	2010-09-12 14:02:43 +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	Fix for DoC issue with multiplexer -- will retire use of multiplexer when	2010-09-07 00:44:07 +00:00
perl	- Update DoC to support output to /dev/null.	2010-09-08 23:43:18 +00:00
python	more useful reports	2010-09-12 14:03:44 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	More Queue scripts for analysis	2010-09-12 14:04:10 +00:00
settings	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
shell	continuing improvements to the queueStatus helper script	2010-09-12 14:04:59 +00:00
testdata	and add changes to the vcf used in testing	2010-06-25 02:56:02 +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	- Include the fasta index builder in the package.	2010-09-08 20:37:54 +00:00
ivy.xml	Okay, finally done with VCF compression. Now:	2010-08-24 16:36:54 +00:00