gatk3的最后一个经典版本3.8
 
 
 
 
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hanna 022601b1a5 Warnings for walkers w/o Javadoc.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2683 348d0f76-0448-11de-a6fe-93d51630548a
2010-01-25 20:34:50 +00:00
R AnalyzeAnnotations now outputs plots with log x-axis in addition to standard x-axis so things like DP and MQ0 are easier to see. AnalyzeAnnotations now skips over all annotations that aren't floating point values. Recalibrator now warns users if PL tags are missing and so therefore it is reverting to illumina. 2010-01-25 19:39:18 +00:00
archive Home for retired duplicateQuals analysis utility 2010-01-06 15:05:00 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc moved to wiki 2009-07-22 16:35:23 +00:00
java Warnings for walkers w/o Javadoc. 2010-01-25 20:34:50 +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 Temporary solution: add the commons logging implementation to the VariantFiltration package. Downstream solution is described in GSA-262. 2010-01-23 01:46:18 +00:00
perl /tmp is failing... 2009-10-08 18:13:49 +00:00
python A collection of python objects that are useful for VCF validation. Use 'em or don't. 2010-01-25 18:44:10 +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 New Picard and SAM-JDK with automatic sequence name truncation 2010-01-11 20:49:13 +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 Warnings for walkers w/o Javadoc. 2010-01-25 20:34:50 +00:00
ivy.xml New VariantFiltration. 2009-11-20 19:50:26 +00:00