gatk3的最后一个经典版本3.8

kshakir 787e5d85e9 Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'. ... Added an initial test for genotyping chr20 on ten 1000G bams. Since tribble needs logging support too, for now setting the logging level and appending the console logger to the root logger, not just to "org.broadinstitute.sting". Updated IntervalUtilsUnitTest to output to a temp directory and not the SVN controlled testdata directory. Added refseq tables and dbsnps to validation data in BaseTest. Now waiting up to two minutes for gather parts to propagate over NFS before attempting to merge the files. Setting scatter/gather directories relative to the -run directory instead of the current directory that queue is running. Fixed a bug where escaping test expressions didn't handle delimiters at the beginning or end of the String. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4717 348d0f76-0448-11de-a6fe-93d51630548a		2010-11-22 22:59:42 +00:00
R	Actually subsets the resulting table now, like it was supposed to all along.	2010-11-17 16:18:23 +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	Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'.	2010-11-22 22:59:42 +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	Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release.	2010-11-18 02:33:45 +00:00
perl	Package all walkers in org/broadinstitute/sting/gatk/walkers directory in release.	2010-11-18 02:33:45 +00:00
python	calling pipeline for v13 of the paper calls -- the final version	2010-11-22 21:57:12 +00:00
ruby	accidentally commited an old tool	2010-08-25 15:42:02 +00:00
scala	Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'.	2010-11-22 22:59:42 +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	Useful script for me	2010-11-18 15:21:06 +00:00
testdata	VQSR now operates on LOD scores in the INFO field directly, and doesn't adjust the QUAL field. New format for tranches file uses LOD score. Old file format no longer supported. log10sumlog10() function, a very useful utility in MathUtils. No more ExtendedPileupElement! Robust math calculations in GMM so that no infinities are generated! HaplotypeScore refactored to enable use of filtered context. Not yet enabled... InferredContext getDouble and getInteger arguments now parse values from Strings if necessary	2010-11-15 22:19:22 +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	Added the ability to test pipelines in dry or live mode via 'ant pipelinetest' and 'ant pipelinetest -Dpipeline.run=run'.	2010-11-22 22:59:42 +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