gatk-3.8

gatk3的最后一个经典版本3.8

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chartl c1263e841c stop printing the debug info -- hurr Also it turns out that sometimes there can be a call with zero total non-I/non-D bases -- so add one to numerator and denominator to prevent divide by zero error git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2262 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-04 16:17:38 +00:00
R	Histogram of covariate values now goes from 0 to max value which makes it look nicer in most cases.	2009-12-04 14:44:03 +00:00
archive	More archiving (with permission from Andrey) plus a move to core.	2009-12-03 15:40:27 +00:00
c	Add a Unix-standard version number to the file.	2009-11-23 20:07:17 +00:00
doc	moved to wiki	2009-07-22 16:35:23 +00:00
java	-dbSNP rod should not implement VariantBackedByGenotype since dbsnp records have no genotype data	2009-12-04 14:56:48 +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	Update the location of the DepthOfCoverage tool in the packaging system.	2009-12-03 19:11:53 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	stop printing the debug info -- hurr	2009-12-04 16:17:38 +00:00
ruby	Adding the ruby directory, and a simple script to restart Bamboo	2009-12-03 22:48:48 +00:00
scala/src	Scala walkers can now be build and run like any other walker in the GATK. Added the getUrlsForClasspath to PackageUtils, the Reflections package isn't getting the manifest files from jars in the classpath, and so we weren't seeing any walkers outside of the GenomeAnalysisTK.jar.	2009-11-02 06:02:41 +00:00
settings	Push version number of picard-private-parts	2009-11-25 19:28:57 +00:00
shell	Renaming error to getNegLog10PError(); added Cached clearing method to GL; SSG now has a CallResult that counts calls; No more Adding class to System.out, now to logger.info; First major testing piece (and general approach too) to unit testing of a walker -- SingleSampleGenotyper now knows how many calls to make on a particular 1mb region on NA12878 for each call type and counts the number of calls AND the compares the geli MD5 sum to the expected one!	2009-09-04 12:39:06 +00:00
testdata	GSA-182: Adding support for BED interval files.	2009-10-06 02:45:31 +00:00
build.xml	adding the option to not halt after a test failure; it will still report failure at the end. This makes sense for Bamboo so we know all the tests that fail, not just the first. It is also useful for checking what tests are affected by a change.	2009-12-03 06:19:39 +00:00
ivy.xml	New VariantFiltration.	2009-11-20 19:50:26 +00:00