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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 83b9d63d59 1. Added functionality to the data sources to allow engine to get mapping from input files to (merged) read group ids from those files. 
2. Used said mapping to implement N-way-in,N-way-out functionality in the new indel cleaner.  Still needs more testing (to be done after vacation but preliminary tests look good).
3. Fixes to VCF validator: ignore case when testing VCF reference base against true reference base and allow quals of -1 (as per spec).



git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2773 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-02-04 04:12:49 +00:00
R Making the dotted quartile lines more clear. 2010-02-03 22:23:09 +00:00
archive Moved old EM model to archive 2010-02-01 02:55:32 +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 1. Added functionality to the data sources to allow engine to get mapping from input files to (merged) read group ids from those files. 2010-02-04 04:12:49 +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 Bringing IndelGenotyper back to life 2010-02-03 20:12:49 +00:00
perl /tmp is failing... 2009-10-08 18:13:49 +00:00
python snpSelector now supports min and max q scores. 2010-01-31 19:38:34 +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 Fully qualify the target for the output file so that external build processes (aka firehose) 2010-01-26 23:06:30 +00:00
ivy.xml New VariantFiltration. 2009-11-20 19:50:26 +00:00