gatk-3.8

gatk3的最后一个经典版本3.8

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kshakir 673fa841a4 Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader. Removed obsolete usages of PackageUtils with updated PluginManager. Ported Queue interval utilities written in scala over to Sting's java IntervalUtils. Added a very basic intergration test to ensure that the fullCallingPipeline.q compiles. Added options to specify the temporary directories without having to use -Djava.io.tmpdir (useful during the above integration test). While adding tempDir added options to specify the run directory from the command line, for example "-runDir v1". Upgraded to scala 2.8.1 and updated calls to deprecated functions. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4661 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-12 20:14:28 +00:00
R	Minor improvement	2010-11-12 19:30:54 +00:00
archive	Fisher exact makes a return. Seems to be working properly. Current tagged as a work in progress. Needs to take the filtered context to be truly correct.	2010-10-22 20:35:53 +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	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +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	include the codecs into the RMD indexer that are available in the GATK, not just Tribble	2010-11-11 06:35:04 +00:00
perl	Also removed contig intervals from the pipeline sanity check perl scsript.	2010-10-21 11:23:34 +00:00
python	V1 of the data processing paper, produced results for the manuscript we presented. Commit for archival purposes	2010-11-11 01:43:21 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +00:00
settings	Added status email support with -statusTo. Will send emails on failure of an individual function or success/failure of the whole pipeline.	2010-10-14 15:58:52 +00:00
shell	Inprocess functions by default now log what output files they are running for.	2010-10-07 19:08:02 +00:00
testdata	VariantEval test for tranches file, plus cutting over VE to use the generic Tranches framework	2010-11-12 13:52:40 +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	GSA-413 Explicitly set all compilers to use 512m memory maximum instead of 64m default maximum and running them out of the ant process.	2010-11-09 19:32:19 +00:00
ivy.xml	Updated PluginManager so that during testing Queue can dynamically compile and load separately multiple class directories into the same class loader.	2010-11-12 20:14:28 +00:00