gatk3的最后一个经典版本3.8

depristo dbb8b86ed1 Minor updates to correctly handle emitting FN calls ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2231 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-02 22:53:17 +00:00
R	Changed the sizes of the dots and bars on the plots generated by the R script which is called from AnalyzeCovariates.java	2009-12-02 19:47:48 +00:00
archive	Initial checkin of AnalyzeCovariates.java which replaces analyzeRecalQuals_1KG.py and is updated to use the new Covariates system. It creates similar plots of residual error for each covariate that was used in the calculation. There is also an option to filter out base qualities below a given threshold.	2009-12-02 16:47:35 +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	Simple utilities for dealing with Complete Genomics data	2009-12-02 22:51:41 +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	Removed ReadQualityRecalibrator.xml	2009-12-02 20:14:14 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	Minor updates to correctly handle emitting FN calls	2009-12-02 22:53:17 +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	add VCFTool.jar	2009-12-02 19:04:38 +00:00
ivy.xml	New VariantFiltration.	2009-11-20 19:50:26 +00:00