gatk-3.8

gatk3的最后一个经典版本3.8

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asivache c8c5c176cd -erw argument, begone! Rod traversals are now enabled. current tests pass, more tests for RODWalkers are welcome ;) git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2600 348d0f76-0448-11de-a6fe-93d51630548a		2010-01-15 21:07:49 +00:00
R	Update to AnalyzeCovariates to make the histogram of PairedReadOrder look a little nicer	2010-01-13 20:26:31 +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	-erw argument, begone! Rod traversals are now enabled. current tests pass, more tests for RODWalkers are welcome ;)	2010-01-15 21:07:49 +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	Adding TileCovariate to the GATK-GSA-Pipeline list.	2010-01-15 20:57:13 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	Minor changes (additional info calculated)	2010-01-06 16:41:01 +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	For Alec, and others at the Broad who want to run our unit/integration tests off of gsa1/gsa2: put a ceiling on the amount of memory that integration tests can use. Reduce the memory footprint of the fasta reader test.	2009-12-28 23:42:46 +00:00
ivy.xml	New VariantFiltration.	2009-11-20 19:50:26 +00:00