gatk3的最后一个经典版本3.8
 
 
 
 
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kshakir 4dfed62e7d Generating the Queue GATK extensions using java, then compiling all the Queue scala code at once to allow circular dependencies between existing and generated scala code.
Will see how this behaves for those using IntelliJ as generated source code will disappear during an ant clean.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4425 348d0f76-0448-11de-a6fe-93d51630548a
2010-10-04 19:38:29 +00:00
R Fix to handle situation where there are no filtered variants. 2010-10-04 18:34:01 +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 remove reference to -mrl 2010-10-04 17:27:01 +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 Removed the SequenomValidationConvertor and renamed it VariantValidationAssessor since it no longer handles ped/sequenom files (but instead works on vcfs/variantcontexts). Updated all of the wiki docs, including adding instructions on how to convert ped files to vcf, a la Shaun Purcell. We now officially no longer support ped files everyone. Other misc cleanup in the code. 2010-10-04 02:11:38 +00:00
perl Obsoleted by VariantReport.R 2010-10-04 01:00:59 +00:00
python clean-up the docs a little 2010-09-29 05:02:41 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Sigh. Fix the source of even more UserErrors in the phone home directory: make sure to gunzip the beagle files before passing them into the conversion walker... 2010-10-01 03:28:36 +00:00
settings The battle is over. Picard is revved. 2010-09-03 05:28:01 +00:00
shell Updated from SnakeYAML 1.6 to 1.7. 2010-09-22 19:47:49 +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 Generating the Queue GATK extensions using java, then compiling all the Queue scala code at once to allow circular dependencies between existing and generated scala code. 2010-10-04 19:38:29 +00:00
ivy.xml Updated from SnakeYAML 1.6 to 1.7. 2010-09-22 19:47:49 +00:00