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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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hanna 4c147329a9 Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file 
in GenomeAnalysisTK.jar.  Still no support for actually displaying the archived javadoc.  Also change the approach 
to providing package javadocs: retired the deprecated package.html file in favor of Java1.5-style package-info.java.


git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2263 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-12-04 20:08:41 +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 Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file 2009-12-04 20:08:41 +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 Turn javadoc comments for packages and classes into key/value pairs in a properties file. Embed the properties file 2009-12-04 20:08:41 +00:00
ivy.xml New VariantFiltration. 2009-11-20 19:50:26 +00:00