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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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kshakir 4ed9f437e9 Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts. 
The GAE half has all the walker specific code.  The new "Abstract" GAE has the rest of the logic.
More refactoring to come, with the end goal of having a tool that other java analysis programs (Queue, etc.) can use to read in genomic data.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4339 348d0f76-0448-11de-a6fe-93d51630548a
 		2010-09-23 23:28:55 +00:00
R This is an updated version of the automated data processing report. Each page in the report is a stand alone function, which are linked together with a function which pulls all appropriate data (assuming a standard naming convention) and generates the pdf. This script still need to respond appropriately when it doesn't find the data it needs, database access, and a way of getting some information from sequencing for the tearsheet. 2010-09-23 18:08:16 +00:00
archive Cleaning up playground utils and tests 2010-08-27 01:25:47 +00:00
c Reduce file handle usage. 2010-01-05 18:03:01 +00:00
doc removing the custom reflections library from the libs, and adding a release version. Hopefully this will fix the problem Menachem has been seeing with random JVM crashes. Also 2010-08-19 00:42:37 +00:00
java Sliced the GAE in half like a gordian knot to avoid the constant merge conflicts. 2010-09-23 23:28:55 +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 Fix for DoC issue with multiplexer -- will retire use of multiplexer when 2010-09-07 00:44:07 +00:00
perl - Update DoC to support output to /dev/null. 2010-09-08 23:43:18 +00:00
python Do this the right way 2010-09-19 04:30:48 +00:00
ruby accidentally commited an old tool 2010-08-25 15:42:02 +00:00
scala Updated from SnakeYAML 1.6 to 1.7. 2010-09-22 19:47:49 +00:00
settings The battle is over. Picard is revved. 2010-09-03 05:28:01 +00:00
shell Updated from SnakeYAML 1.6 to 1.7. 2010-09-22 19:47:49 +00:00
testdata and add changes to the vcf used in testing 2010-06-25 02:56:02 +00:00
LICENSE Adding a license to the root directory in case BOSC checks for one. Has the 2010-04-20 16:04:29 +00:00
build.xml Added the new pipeline classes to the StingUtils.jar so that ant test picks them up. 2010-09-22 20:05:22 +00:00
ivy.xml Updated from SnakeYAML 1.6 to 1.7. 2010-09-22 19:47:49 +00:00