gatk3的最后一个经典版本3.8

hanna 87aca64716 Jumped the gun a bit on bam on-the-fly indexing -- Tim says it's not ready yet. ... Turned it off by default and added a property to turn it back on. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4254 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-10 21:16:03 +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	Jumped the gun a bit on bam on-the-fly indexing -- Tim says it's not ready yet.	2010-09-10 21:16:03 +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	Minor usability improvements to reporting tool	2010-09-08 02:56:25 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	At chartl's superb suggestion, command line files are now all Files instead of old method of sometimes "has a File". Should be easier when reassigning them.	2010-09-02 21:30:48 +00:00
settings	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
shell	Useful script to see the status of gsa computing resources. Crontab'd and will be arriving as email at 8 am	2010-08-07 12:36:28 +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