gatk3的最后一个经典版本3.8

scalvo b5c127e643 Removed HAPLOTYPE_STRAND_COLUMN; Previously, GenomicAnnotation allowed a user to specify the strand of the haplotypeAlternate, and would reverseComplement the haplotypeAlternate if HAPLOTYPE_STRAND_COLUMN was "-". The new specification does not allow this functionality, and instead requires both the reference and the alternate haplotypes to be on the + strand (as in VCF format). ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4443 348d0f76-0448-11de-a6fe-93d51630548a		2010-10-06 20:37:41 +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	Removed HAPLOTYPE_STRAND_COLUMN; Previously, GenomicAnnotation allowed a user to specify the strand of the haplotypeAlternate, and would reverseComplement the haplotypeAlternate if HAPLOTYPE_STRAND_COLUMN was "-". The new specification does not allow this functionality, and instead requires both the reference and the alternate haplotypes to be on the + strand (as in VCF format).	2010-10-06 20:37:41 +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	/broad/1KG doesn't exist	2010-10-06 12:54:38 +00:00
perl	update the example: /broad/1KG doesn't exist anymore	2010-10-05 13:50:24 +00:00
python	Shorter outputs, new summary mode	2010-10-06 14:34:50 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Added the ability to Queue to run scala functions inside the JVM. NOTE: Extend from InProcessFunction instead of CommandLineFunction to use this functionality.	2010-10-06 18:29:56 +00:00
settings	The battle is over. Picard is revved.	2010-09-03 05:28:01 +00:00
shell	minor improvements to queue status	2010-10-06 14:34:35 +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	Fixed re-builds of queue so that previously compiled classes are included. Fixes redundant case of "ant queue test" vs. "ant test".	2010-10-04 21:12:07 +00:00
ivy.xml	Updated from SnakeYAML 1.6 to 1.7.	2010-09-22 19:47:49 +00:00