gatk3的最后一个经典版本3.8

delangel ef7454a241 Minor improvements to indel genotyper: ... a) Ability to specify haplotype size from command line b) Expand reference context window so we can form haplotypes for longer indel events. c) small bug fix in temp output writer (to be removed once I can emit vcfs) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4212 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-03 22:52:08 +00:00
R	Better reporting and now with a special mode for listing exceptions	2010-09-01 16:19:51 +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	Minor improvements to indel genotyper:	2010-09-03 22:52:08 +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	Enabling support for any scala used in QScripts.	2010-08-17 22:05:56 +00:00
perl	Removing the obsolete --hapmap and --hapmap_chip options	2010-08-31 16:57:05 +00:00
python	More robust analysis tool	2010-09-01 20:24:04 +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	up the test mem. from 2g to 4g; we're currently hitting the 2g in aggregate across some of the larger tests	2010-08-27 01:39:05 +00:00
ivy.xml	Okay, finally done with VCF compression. Now:	2010-08-24 16:36:54 +00:00