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gatk3的最后一个经典版本3.8
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Java 95.8%
Scala 3.8%
R 0.2%
JavaScript 0.1%
 
 
 
 
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ebanks bd2a46ab4c I want to move over to hpprojects tonight, so I'm checking in various changes all in one go: 
1. Initial code for annotating calls with the base mismatch rate within a reference window (still needs analysis).
2. Move error checking code from rodVCF to VCFRecord.
3. More improvements to SNP Genotype callset concordance.
4. Fixed some comments in Variation/Genotype



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2341 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-12-13 02:52:18 +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 I want to move over to hpprojects tonight, so I'm checking in various changes all in one go: 2009-12-13 02:52:18 +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 - Depth annotation now includes MQ0 reads 2009-12-09 02:53:00 +00:00
perl /tmp is failing... 2009-10-08 18:13:49 +00:00
python Better support for reading truth file 2009-12-10 12:16:05 +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 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 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