gatk3的最后一个经典版本3.8

asivache 1f64c5d41a Do not slurp the whole set of snp mask sites into memory (gets pretty heavy on full dbSNP!); instantiate a privare ROD iterator instead and drag it across the sites we are designing probes for. ... git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2694 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-26 22:39:46 +00:00
R	AnalyzeAnnotations can now process only variants that are found in samples that match the -sampleName argument. X-axis of plots no longer use annoying scientific notation.	2010-01-25 20:52:11 +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	Do not slurp the whole set of snp mask sites into memory (gets pretty heavy on full dbSNP!); instantiate a privare ROD iterator instead and drag it across the sites we are designing probes for.	2010-01-26 22:39:46 +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	Now using the new VariantEval package.	2010-01-26 16:32:44 +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