gatk3的最后一个经典版本3.8

asivache 21a34daf2e add playground classes to the jar (if they are compiled). Thanks, Khalid! ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4317 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-20 22:28:08 +00:00
R	improvements to the report code	2010-09-15 00:45:13 +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	Cleanup: Use Tribble's version of createVariantContextWithPaddedAlleles (no real functional difference) to avoid duplicated code.	2010-09-20 19:53:30 +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	Do this the right way	2010-09-19 04:30:48 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Fix for Matt: For Mac OS 10.6 temporary directories replace paths like '/var/folders/Ax/AxRUoz51Fh05fVe-j6C1Wk+++TI/-Tmp-/' with '/tmp/' so that google reflections 0.95RC2 still works on classes in the directory.	2010-09-20 22:02:07 +00:00
settings	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
shell	Fixed header generation when lines contain spaces.	2010-09-17 17:14:59 +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	add playground classes to the jar (if they are compiled). Thanks, Khalid!	2010-09-20 22:28:08 +00:00
ivy.xml	Adding the --sample-metadata (-SM) command line argument and associated functionality. This is something Matt and I have been working on for a while. Basically, it allows you to integrate sample metadata into an analysis, by including a sample file. More detailed documentation is on the wiki: http://www.broadinstitute.org/gsa/wiki/index.php/Adding_Sample_data_to_an_analysis	2010-09-15 11:50:22 +00:00