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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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kiran e4770885fd The four-probs for all bases in a single read. Some utility functions for generating the primary and secondary base strings, as well as generating the SQ tag byte array in a manner that's consistent with the Bustard base calls (meaning the primary Bustard call and the secondary Four-Prob call are not permitted to be the same). 
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@704 348d0f76-0448-11de-a6fe-93d51630548a
 		2009-05-14 16:55:49 +00:00
c Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
doc Added documentation for calling the GATK from Matlab. This is to document the extreme basic and experimental support for using Matlab to call the GATK, and is more of a placeholder for when we have time to revisit supporting this. 2009-05-13 15:25:51 +00:00
java The four-probs for all bases in a single read. Some utility functions for generating the primary and secondary base strings, as well as generating the SQ tag byte array in a manner that's consistent with the Bustard base calls (meaning the primary Bustard call and the secondary Four-Prob call are not permitted to be the same). 2009-05-14 16:55:49 +00:00
python Reference-ordered data relies on bugs in the old command-line argument system to work. Update the ROD system to from -B track1 type1 file1 track2 type2 file2 to -B track1,type1,file1 -B track2,type2,file2. 2009-05-08 15:28:19 +00:00
settings Bumped sam to latest. 2009-05-13 19:19:55 +00:00
shell Move non-java code out of playground. 2009-03-23 19:31:38 +00:00
testdata Better validation scripts and data 2009-04-29 17:40:07 +00:00
build.xml Added IterableLocusContextQueue and test. Cleaned up tests, adding BaseTest where it didn't exist. Enhanced test runner to run only classes ending in ...Test.java, so that utility classes can sit alongside the tests but won't be run by JUnit. 2009-05-13 21:32:05 +00:00
ivy.xml Change the sample XML marshalling code over to simple XML, and take out the castor lines in the ivy.xml 2009-05-08 00:08:25 +00:00