gatk-3.8

gatk3的最后一个经典版本3.8

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alecw 159778416c In TableRecalibrationWalker, update UQ tag if it was present in the original SAMRecord. This required a new sam.jar, which caused some other files to need to be changed. git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2435 348d0f76-0448-11de-a6fe-93d51630548a		2009-12-23 21:42:36 +00:00
R	R script for graphing depth of coverage by sample name, and generating a loess curve for each sample's data.	2009-12-10 21:58:01 +00:00
archive	Move VariantAnnotator over to use a StratifiedAlignmentContext split by sample.	2009-12-11 05:28:28 +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	In TableRecalibrationWalker, update UQ tag if it was present in the original SAMRecord. This required a new sam.jar, which caused some other files to need to be changed.	2009-12-23 21:42:36 +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 a package description for making a version of the GATK that only includes the FixBAMSortOrderTag walker.	2009-12-22 00:35:24 +00:00
perl	/tmp is failing...	2009-10-08 18:13:49 +00:00
python	Updated SNP calling power from coverage tools to work with new UnifiedGenotyper and DepthOfCoverage tools.	2009-12-16 20:44:30 +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	In TableRecalibrationWalker, update UQ tag if it was present in the original SAMRecord. This required a new sam.jar, which caused some other files to need to be changed.	2009-12-23 21:42:36 +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	Clean up some of the walker help output based on additional experience and	2009-12-07 21:33:11 +00:00
ivy.xml	New VariantFiltration.	2009-11-20 19:50:26 +00:00