gatk3的最后一个经典版本3.8

ebanks 4e83ba411f We now do lazy loading for the genotype data in VCF. Practically, almost all walkers end of loading the genotype data because we need to be smarter about transfering the unparsed genotype string when modifying VariantContexts; however, this does solve the problem for VR's piece to generate clusters (shaved off 75% of runtime for Ryan's large case). That further optimization will happen later. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4279 348d0f76-0448-11de-a6fe-93d51630548a		2010-09-15 00:18:17 +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	We now do lazy loading for the genotype data in VCF. Practically, almost all walkers end of loading the genotype data because we need to be smarter about transfering the unparsed genotype string when modifying VariantContexts; however, this does solve the problem for VR's piece to generate clusters (shaved off 75% of runtime for Ryan's large case). That further optimization will happen later.	2010-09-15 00:18:17 +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	Fix for Queue	2010-09-12 15:18:08 +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